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authorJustin Lecher <jlec@gentoo.org>2011-12-20 08:39:39 +0000
committerJustin Lecher <jlec@gentoo.org>2011-12-20 08:39:39 +0000
commit6b4ae6f9753bfe698b67cd262c7197e99436fcf0 (patch)
treeb75a02a825e8ec0a683784473cfe3b283dae4b73 /sci-chemistry
parentVersion bump. Removed old (diff)
downloadhistorical-6b4ae6f9753bfe698b67cd262c7197e99436fcf0.tar.gz
historical-6b4ae6f9753bfe698b67cd262c7197e99436fcf0.tar.bz2
historical-6b4ae6f9753bfe698b67cd262c7197e99436fcf0.zip
Todays Python Patches, cleaned old
Package-Manager: portage-2.2.0_alpha81/cvs/Linux x86_64
Diffstat (limited to 'sci-chemistry')
-rw-r--r--sci-chemistry/ccpn/ChangeLog18
-rw-r--r--sci-chemistry/ccpn/Manifest50
-rw-r--r--sci-chemistry/ccpn/ccpn-2.1.5_p110602.ebuild213
-rw-r--r--sci-chemistry/ccpn/ccpn-2.1.5_p110629.ebuild213
-rw-r--r--sci-chemistry/ccpn/ccpn-2.1.5_p110817.ebuild213
-rw-r--r--sci-chemistry/ccpn/ccpn-2.1.5_p110905.ebuild213
-rw-r--r--sci-chemistry/ccpn/ccpn-2.1.5_p110926.ebuild220
-rw-r--r--sci-chemistry/ccpn/ccpn-2.1.5_p111011.ebuild214
-rw-r--r--sci-chemistry/ccpn/ccpn-2.1.5_p111017.ebuild214
-rw-r--r--sci-chemistry/ccpn/ccpn-2.1.5_p111028.ebuild214
-rw-r--r--sci-chemistry/ccpn/ccpn-2.1.5_p111220.ebuild (renamed from sci-chemistry/ccpn/ccpn-2.1.5_p111124.ebuild)2
-rw-r--r--sci-chemistry/ccpn/ccpn-2.2.1_p110602.ebuild213
-rw-r--r--sci-chemistry/ccpn/ccpn-2.2.1_p110629.ebuild213
-rw-r--r--sci-chemistry/ccpn/ccpn-2.2.1_p110817.ebuild213
-rw-r--r--sci-chemistry/ccpn/ccpn-2.2.1_p110905.ebuild213
-rw-r--r--sci-chemistry/ccpn/ccpn-2.2.1_p110926.ebuild220
-rw-r--r--sci-chemistry/ccpn/ccpn-2.2.1_p111011.ebuild214
-rw-r--r--sci-chemistry/ccpn/ccpn-2.2.1_p111017.ebuild214
-rw-r--r--sci-chemistry/ccpn/ccpn-2.2.1_p111019.ebuild214
-rw-r--r--sci-chemistry/ccpn/ccpn-2.2.1_p111028.ebuild214
-rw-r--r--sci-chemistry/ccpn/ccpn-2.2.1_p111220.ebuild (renamed from sci-chemistry/ccpn/ccpn-2.2.1_p111124.ebuild)2
21 files changed, 27 insertions, 3687 deletions
diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index b0b7f0fd0413..e1be611d98f2 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,22 @@
# ChangeLog for sci-chemistry/ccpn
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.76 2011/12/13 08:33:36 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.77 2011/12/20 08:39:39 jlec Exp $
+
+*ccpn-2.2.1_p111220 (20 Dec 2011)
+*ccpn-2.1.5_p111220 (20 Dec 2011)
+
+ 20 Dec 2011; Justin Lecher <jlec@gentoo.org> -ccpn-2.1.5_p110602.ebuild,
+ -ccpn-2.1.5_p110629.ebuild, -ccpn-2.1.5_p110817.ebuild,
+ -ccpn-2.1.5_p110905.ebuild, -ccpn-2.1.5_p110926.ebuild,
+ -ccpn-2.1.5_p111011.ebuild, -ccpn-2.1.5_p111017.ebuild,
+ -ccpn-2.1.5_p111028.ebuild, -ccpn-2.1.5_p111124.ebuild,
+ +ccpn-2.1.5_p111220.ebuild, -ccpn-2.2.1_p110602.ebuild,
+ -ccpn-2.2.1_p110629.ebuild, -ccpn-2.2.1_p110817.ebuild,
+ -ccpn-2.2.1_p110905.ebuild, -ccpn-2.2.1_p110926.ebuild,
+ -ccpn-2.2.1_p111011.ebuild, -ccpn-2.2.1_p111017.ebuild,
+ -ccpn-2.2.1_p111019.ebuild, -ccpn-2.2.1_p111028.ebuild,
+ -ccpn-2.2.1_p111124.ebuild, +ccpn-2.2.1_p111220.ebuild:
+ Todays Python Patches, cleaned old
*ccpn-2.2.1_p111213 (13 Dec 2011)
*ccpn-2.1.5_p111213 (13 Dec 2011)
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 1489f0c83a2d..b3f9cff13393 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -19,55 +19,21 @@ DIST analysis2.1.3_1.tar.gz 18932918 RMD160 5f19ea6fe47c2910d16fcba8d1a78f0e1dea
DIST analysis2.1.5.tar.gz 20338459 RMD160 b0706c859c1ee4da2ab80ee41534197268f73d44 SHA1 70dc5e6b2752d6b7d5c8673fc992ebd0a88e6ad0 SHA256 9f91f1bd56fb73fd24e71d396c96c0f0d31b92287664b6a2e756f6efc630b31b
DIST analysis2.2.1.tar.gz 20974926 RMD160 5905f43fc1399a656f018808c4a2f8dd3d247ca9 SHA1 eed30da55a719ef6c29431e3b3c5a76f521010dc SHA256 d1252811b3db3a30d96a73368bae8abcb05de02fcd2f1f9c502d71dff5e00d13
DIST ccpn-update-100806.patch.bz2 187965 RMD160 3297162fe3314aa405ee58737ce45cda084834e5 SHA1 338423d9f36da3fb10dc9d9a3b8aeb932ae3bfd0 SHA256 5cea7899edb96237a6674f04a1beee6ad7b309e12964ea8b25d9ea6ff752d0d4
-DIST ccpn-update-2.1.5-110602.patch.bz2 81505 RMD160 2af0d5ca21828ccc3345ec763edfce81f2e12d11 SHA1 cf4a8613ecbb11421a4fb007500a6090b017fb2f SHA256 c8880d295914ac95c2ae2f0ffe3eb57e0e2b1b6c3c573eb31c8a40852c5cb886
-DIST ccpn-update-2.1.5-110629.patch.bz2 86224 RMD160 d4cb190ce84f62639d77f6592475746e8b9f6a0e SHA1 e20f3313853dff4a3de723a2efc70efe81c63861 SHA256 df847050c95ea925db16a5c6630861e308d39286cc7c207efc4360fce53e29b2
-DIST ccpn-update-2.1.5-110817.patch.bz2 88191 RMD160 9fe24e51a1416cdde25ac6d25c2764840c1a00ef SHA1 d16956e6ad7530d17c9e46b877eaf993959f49a2 SHA256 176fd4488c40d7eb426df353d85a05ddb8e4b4126f32264c9d536bf1799fe44c
-DIST ccpn-update-2.1.5-110905.patch.bz2 99670 RMD160 d3163c0d2d07661e318fa101267ef9dba6d05244 SHA1 3b61f72e66bf56c8c2799b864eef91643a30f367 SHA256 c2fa8f6c3f9826747e9f244a46b7ab701ff83dabc36f8ae534db0d76239c5da9
-DIST ccpn-update-2.1.5-110926.patch.bz2 99882 RMD160 8e1aa7563ea395c9ef68c87fb4d400d8d8ddc3ec SHA1 efafa90ae1edd7bf0be0bffad76c27c514b47213 SHA256 cff2cec1728fa92636ec4b89d638238755ae055c12b8453298c3ee9daceac012
-DIST ccpn-update-2.1.5-111011.patch.xz 103208 RMD160 475d1f1bba8e72c2e30340d3ab33969206a7e22b SHA1 b05f14ba39d14f67b879b1c190eac024278d9c27 SHA256 6e07a122f3353522c5abf3e02739aa792538403674393192b3f0b86f68a067d3
-DIST ccpn-update-2.1.5-111017.patch.xz 103212 RMD160 5ca2023fe7cb29f2989b9f56e7d0a1594d835c42 SHA1 c77d66ff9521c1e796c75e8719e85048126d2d95 SHA256 7485e59ad4cffcc4139a913b17afcdba971967c871a512c4afdf76c580f339a5
-DIST ccpn-update-2.1.5-111028.patch.xz 103400 RMD160 2dbfc857edf38d75f48fda887378b4565e59d43d SHA1 98625971247eb169d13a52ad6b774b0578fb8f8c SHA256 d7ae6e5e0a7e75901f0713a7d44bd00bb48fa5402ab6caf4cf4c7ca9e50125e5
-DIST ccpn-update-2.1.5-111124.patch.xz 104712 RMD160 43f4c96d295e9fe98484ea78413e430e64e61acc SHA1 85a47fc245e0a5ff9a54c3d48696cc4b1c5e9b7c SHA256 e227124fead5df83ea8e0ff7ecefcd2e49743b492c606f4d58781d2481280012
DIST ccpn-update-2.1.5-111213.patch.xz 104892 RMD160 d2a83a0b809a91f8f8422a24c11ce20a8e2cde8d SHA1 ae819afdf4cb6aa39c9059cd1bb96d3d188a86fb SHA256 72bbe7f2a68ee20eca029685b8b3daaf15f71d164767b3aa5d222c3a5de779b1
-DIST ccpn-update-2.2.1-110602.patch.bz2 57084 RMD160 502c9ca948caf7be5e87759222982a952dd81bc2 SHA1 31725499eba0bb851357227fc4db274121a32240 SHA256 591be1c0c5dfea56c7fa8aec5da154a2a7263a11e8e20ff2a71a2e6e484c6e00
-DIST ccpn-update-2.2.1-110629.patch.bz2 66050 RMD160 8d3b37d9c848f177b4c35f36eccd1026500af0b4 SHA1 66371f52b15ec8c689c1634fa30f6679c4e8c681 SHA256 99280022b594a45d1bdb9811f0f78851a8cb8282476c521987def7ab13cb0dac
-DIST ccpn-update-2.2.1-110817.patch.bz2 77149 RMD160 69c2417ca700129d9c53f90d5be665b2192ae0c0 SHA1 b61874c4753251ac08fd4549f6b656352e462ece SHA256 f08b1082435546c605d516167617cdf5b163aa820150718fa8e205cd4f9a3232
-DIST ccpn-update-2.2.1-110905.patch.bz2 78329 RMD160 295a3057f4ccd0ad89a3bc75a9992351953be891 SHA1 b7f1e545777d5850564475ce5fb495c0f516a748 SHA256 e3823d29f58a2f6adb3a1855c6665604d8cff8a7f26af75f2b8c6c990a58a36f
-DIST ccpn-update-2.2.1-110926.patch.bz2 79805 RMD160 2eb19fe8cc1bcf98dba2aa892f41cef16ababd01 SHA1 09199cec4c733befb32558d5138fff93a94fa03f SHA256 5e8b44399cb0fd3b0a20405c3c65428aefd3a47445a003e40f4caac2fe77fd41
-DIST ccpn-update-2.2.1-111011.patch.xz 76948 RMD160 1bac8433d91adb373971a4130bb9a89cf46a4051 SHA1 a6001349d0da0bcf9f1142c5b4050ad1903fdf0d SHA256 ec7fc527d6f869f2a952e52e73a4ea17a257237e9724e4916119ba484688aeeb
-DIST ccpn-update-2.2.1-111017.patch.xz 76984 RMD160 26a58d486bdc33cafaced593c327a00162b6605a SHA1 e8503957efaa6deb53c8537b954ec2ce972a6bc4 SHA256 73e38c80b38957a9484e885cb4c867f67d17b43ff61a5f25ad35d6c9fddd3e7a
-DIST ccpn-update-2.2.1-111019.patch.xz 68036 RMD160 6481ae9b2ba14f1084e33a7cfde6d75d690cbc84 SHA1 3d0227376ac2d67a421dc9e00cb4a276be8ad671 SHA256 e812aeec0d065e69b59567bb3e1b9d3d47968665bd223edbbd92c74ec811bdc9
-DIST ccpn-update-2.2.1-111028.patch.xz 78540 RMD160 4a496dac05b2cc787b7ad27aabf2f22542ff8656 SHA1 25270b1ff71997b766a4fc6b87340016f4e9b6a5 SHA256 31cca8ddd372a45ea0b97d9629918c09e581883eef344685a4fa500874aa8634
-DIST ccpn-update-2.2.1-111124.patch.xz 81296 RMD160 3cbcd233e037d5608140766c20d26365583e6222 SHA1 a8e8e7d1881d10186bd50295453753776ff5892a SHA256 d03d9f9a5834a412660220e1979c257166f112f40437c934030f4831c2c07fe7
+DIST ccpn-update-2.1.5-111220.patch.xz 105472 RMD160 f8c358e7bc7757a4f645a2f26fa38e0159e5bc2f SHA1 21721845d3f0df77c548a3e5774ed5a82f3d12df SHA256 a4d8d4982c8bf63031cd11cbe67121a598b97f1c490862c363555bf9c2f11140
DIST ccpn-update-2.2.1-111213.patch.xz 81520 RMD160 55038a1272f8e01ce54fefdba081ee51ec5d4f36 SHA1 0bbd8c029a98b282002d8b5385a85355722de323 SHA256 807cef8e8b2822e178d50695c7e234ea8c243264a4711610f6a95e30e1b40d12
+DIST ccpn-update-2.2.1-111220.patch.xz 82840 RMD160 c0fb328ad93d7f07e1f0d45215d7686204315f91 SHA1 7b2ef76c62e85fcb4c5c95be053a9e281bc3d59d SHA256 f8942568e4f859da71e5a38b279355222882de19328501a0297bcddefef75c9f
EBUILD ccpn-2.1.3.1_p100806.ebuild 5188 RMD160 b66825e37b79a5f6ec6635b9f3236d1cda2da672 SHA1 458f516ffad25d9283b21c9dfb8e50c6323f4264 SHA256 ff57abefefd3bb128a3f96bf039cbaa5ed97350f6b41fdbdd4b4365ff9e68e51
-EBUILD ccpn-2.1.5_p110602.ebuild 5802 RMD160 b979b28541d4a52d52df45af0ac194c147e9e586 SHA1 bf731d3e076684670155ea7ed6f862785c961130 SHA256 a5b205266d47c77f3bcb2f4149a53e2866a665d28e49b5749dd0d3774d50cc38
-EBUILD ccpn-2.1.5_p110629.ebuild 5802 RMD160 99ce3cef5396276532ab3301e5442f72c379e39e SHA1 9efbd6e35633b15b92449228c17a82890d394c38 SHA256 f29088839b852119b20caa877a105aa4af4a447d60c429b8c7bd92e0918a9ea1
-EBUILD ccpn-2.1.5_p110817.ebuild 5802 RMD160 112485a848b98a5f8377b2d05c8555147de6dfd5 SHA1 1dfab5862dc3890a5d131f1f6e78c8f28f797ac1 SHA256 135ccefec5d55bedc301c2e9d1d61e31b09f17daec2d835f7f6e9f50272a42e9
-EBUILD ccpn-2.1.5_p110905.ebuild 5802 RMD160 4213a4957af30e78714604bed3cc565acc172a71 SHA1 579587f639367f3988f9f1925e78751bad08ad41 SHA256 dcf706cbadac4352090d7650838af11e0d5c03c6b42d71ba7d4906847b248f92
-EBUILD ccpn-2.1.5_p110926.ebuild 6010 RMD160 b1c16c451387a7f6aec29662843d79fa5ebbdd6e SHA1 e8c9aa2b897b7c0fff10cda35ce4cf6f561d2edf SHA256 0fd5352daa50a772138bff644cc3db9317cfbbb7dd4a2eea4bf02dd4487714a6
-EBUILD ccpn-2.1.5_p111011.ebuild 5766 RMD160 2de7124aa015e929939a35372841eca6b9c6b760 SHA1 d9d40612897662548f67fc05bf19a65ce893c8eb SHA256 1826ca6259f1f58f0b34d8e9baa785d4542e8cdd926370a9be4b36f9d0fc256b
-EBUILD ccpn-2.1.5_p111017.ebuild 5773 RMD160 74770cdc30a513ca57b66667b9377883cc25ffd4 SHA1 1cc1c784d1921c3922a98548fc4f219327725248 SHA256 5da3935144bbb0b01bc826218c9b92de1148f799a0bd5965f83ca753cc7391e2
-EBUILD ccpn-2.1.5_p111028.ebuild 5773 RMD160 71c046eb48f2c1c88e619c4a7cb66ab08a792477 SHA1 9bd4d196cd738e823ef8e118e1620541f7a328fd SHA256 0285a567273fae510d241fc378be5822eef0f7b4319723d5df4e8803ea0f4a10
-EBUILD ccpn-2.1.5_p111124.ebuild 5773 RMD160 40602ef32b4690fc7cc940199f5a18f765d9ee79 SHA1 982e51c9cdcb02b292eebe546a9192f8adb81e01 SHA256 978cbd154039ca80c0b4fdcd11f93ba19f0b7edc7137147488b81177728220e6
EBUILD ccpn-2.1.5_p111213.ebuild 5773 RMD160 4fc120d9e6c5ecfd375a3df14a7b8b9afdebb3b5 SHA1 30bb2d2e22087ac6c93434863f1347db50f2514f SHA256 46de0ddcfd2fcb196dfb9ceb07c74c25ff3c8f4655b55f5e4b2f1d90a3787641
-EBUILD ccpn-2.2.1_p110602.ebuild 5817 RMD160 02a268d39e592e55955bd768c13d486fa37394df SHA1 4d419c6825b3eba1bbc9d1f21a441fee54633dcf SHA256 d01e038bb78efe67639c2fe0571f17ead32fb931cc14bf3f1a2d0140e322557c
-EBUILD ccpn-2.2.1_p110629.ebuild 5817 RMD160 10a004a5f52097e30cceef012832dc31ac4a35ee SHA1 7d23a32e384549d53ab406c5e2ff96d6984e8b9c SHA256 99cb9b2c41b7c6cbb8405177b9d99b1c06ad140059bfa001ffbae68bc150b636
-EBUILD ccpn-2.2.1_p110817.ebuild 5817 RMD160 e9302ad7cb2e95a8c2e24359691a3c2371402a89 SHA1 923d0a52f358bf45de72d6b71fcb519f187f9298 SHA256 67c4e3e30cb978b5eb879ad532f3b30d3afcd14b3019bb5d27c779607914448c
-EBUILD ccpn-2.2.1_p110905.ebuild 5817 RMD160 d3f9cc71971395a5e7b907c7081851d756f9ced8 SHA1 dd8c79e2b29af8f9de92edf4b0e9425f13fd6203 SHA256 4b8d550918003a3f3e25c043ed2625ea634c08ffc353a6354579a235c7a1e2a1
-EBUILD ccpn-2.2.1_p110926.ebuild 6025 RMD160 c8fbfe5b3e10a79447e86ff3fd49f1e7c5eb44d0 SHA1 dd9f901354a019ed1bb1731548264d3c8cfd833c SHA256 5b76872a98bb9e63db70bc96b22fd8acdf719c665e10a3e404af431f8693783d
-EBUILD ccpn-2.2.1_p111011.ebuild 5781 RMD160 078beee165b07aa92753a05312179edc6ed82e2d SHA1 379e2840780bb9b5f86e8ddf134eec03174a93e3 SHA256 eb6ad46393d8e0efd724dd5d966363c2aa17c4ccef30b4c3a6de62f35970fb2c
-EBUILD ccpn-2.2.1_p111017.ebuild 5788 RMD160 f83ad913229aeb54667bf55ec2d5b1563b511492 SHA1 9dbce4e6f7c1e90e84fc389873261410e882fc1d SHA256 6a85c4e9c4ca84325bd2cb6627b7f82d0d245a893ab43bd8fdb39fed74f2876a
-EBUILD ccpn-2.2.1_p111019.ebuild 5788 RMD160 1199938733ab49962a7cda42f86cb9d1d4d99840 SHA1 ebed2c4883b8c8c4f3788ba4b160df136b1c5d35 SHA256 08dc643197243a4836c440c37258be1651fe1d8b96d46ef4da668ae03d65cdd3
-EBUILD ccpn-2.2.1_p111028.ebuild 5788 RMD160 c9d9075636aa52e8e92d3fb1ab7f0800bcfdc3ef SHA1 bb2a99f8bef3327ed15bc118304aec4210a52024 SHA256 bf0fbf5f6558d780925e95b722575f1c3d32607244af1f744c85f58f452fa4ed
-EBUILD ccpn-2.2.1_p111124.ebuild 5788 RMD160 67c30d743b838b890dd3499e36f28b0380e9e644 SHA1 37ea9409000485c057cbbd7d160e02f783b1b3fd SHA256 23aa3778bf05b3bc9a21bcbc79f2bd17516c0b1a82ecd078a8ca6988a846201d
+EBUILD ccpn-2.1.5_p111220.ebuild 5773 RMD160 726f13ab2aa4532df15cbdc5a96b15293e53791e SHA1 5038f1c70ee0979181278ad3bbc9cdafff54d81c SHA256 7c21ffd5368b3a1c46ee838be8b970c6f7af371ea1048a253eca9c4c73af40c8
EBUILD ccpn-2.2.1_p111213.ebuild 5788 RMD160 49f50c489d3eee93f80e1548c66fe2acf1131e20 SHA1 fe36614826a38746d32f32071f8583744fa263fd SHA256 2f25c2e6e348f37d95bc89dc36137303def1c66a02ff1603eedb8c32f61867e4
-MISC ChangeLog 15010 RMD160 69c0a89d67873d1ed305f172bdeeda14de6671e4 SHA1 08af23375e54832c13b03edecd575aed79a5ca62 SHA256 c717826240b6edf5f6a573e219eda7db43c0c7fef4595d72e635d53d1c2746f2
+EBUILD ccpn-2.2.1_p111220.ebuild 5788 RMD160 abb85d91207669ef94be18d38b4e9efc5dca135b SHA1 e07108a62c4867be2d4538a0ecf09bf5ac4dd968 SHA256 37885cacf0a4e97d05201b18949b87889c5e5965f04434399a2e52b24d30cf98
+MISC ChangeLog 15772 RMD160 c68edc0742245f733471de2f8a86ece12bf87eaa SHA1 d89dbad83be0b61e2d45f28aa8880ac6cd3b2e41 SHA256 cc398ca99864b9d79c0e4d305c0e73b535b35ed265b79859e6d148e9ca936667
MISC metadata.xml 322 RMD160 9fd5fba7405b689fc39a089d81ffdaa9f961b514 SHA1 0c31132b25fca04cff97ef11fdc11940f90c77d0 SHA256 7468ba4c27b879e7ed5f82274f5837e51f1f389673a33b9e26e1756a6b0783df
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diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p110602.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p110602.ebuild
deleted file mode 100644
index faf270c21216..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.1.5_p110602.ebuild
+++ /dev/null
@@ -1,213 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p110602.ebuild,v 1.3 2011/10/07 19:29:31 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-PYTHON_USE_WITH="ssl tk"
-
-inherit eutils portability python toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
- [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.bz2"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="extendnmr +opengl"
-
-RDEPEND="
- dev-lang/tk[threads]
- >=dev-python/numpy-1.4
- >=dev-tcltk/tix-8.4.3
- =sci-libs/ccpn-data-"${MY_MAJOR}"*
- x11-libs/libXext
- x11-libs/libX11
- opengl? (
- media-libs/freeglut
- dev-python/pyglet )"
-# We need to fix this
-# sci-chemistry/mdd
-DEPEND="${RDEPEND}"
-PDEPEND="
- extendnmr? (
- <=sci-chemistry/aria-2.3.2
- sci-chemistry/prodecomp )"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
- epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
- local tk_ver
- local myconf
-
- tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
- if use opengl; then
- GLUT_NEED_INIT="-DNEED_GLUT_INIT"
- IGNORE_GL_FLAG=""
- GL_FLAG="-DUSE_GL_TRUE"
- GL_DIR="${EPREFIX}/usr"
- GL_LIB="-lglut -lGLU -lGL"
- GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
- GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
- else
- IGNORE_GL_FLAG="-DIGNORE_GL"
- GL_FLAG="-DUSE_GL_FALSE"
- fi
-
- GLUT_NOT_IN_GL=""
- GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
- rm -rf data model doc license || die
-
- sed \
- -e "s|/usr|${EPREFIX}/usr|g" \
- -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
- -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
- -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
- -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
- -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
- -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
- -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
- -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
- -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
- -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
- -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
- -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
- -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
- c/environment_default.txt > c/environment.txt
-}
-
-src_compile() {
- emake -C c all links || die
-}
-
-src_install() {
- local libdir
- local tkver
- local _wrapper
-
- find . -name "*.pyc" -type d -delete
-
- libdir=$(get_libdir)
- tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
- _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara"
- use extendnmr && _wrapper="${_wrapper} extendNmr"
- for wrapper in ${_wrapper}; do
- sed \
- -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
- -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
- -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
- -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
- -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
- -e "s|//|/|g" \
- "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
- dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
- done
-
- local in_path
- local files
- local pydocs
-
- pydocs="$(find python -name doc -type d)"
- rm -rf ${pydocs} || die
-
- in_path=$(python_get_sitedir)/${PN}
-
- for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
- sed \
- -e 's|#from __future__|from __future__|g' \
- -i ${i} || die
- done
-
- insinto ${in_path}
-
- dodir ${in_path}/c
-
- ebegin "Installing main files"
- doins -r python || die "main files installation failed"
- eend
- dosym ../../../..//share/doc/ccpn-data-${MY_MAJOR}/html ${in_path}/doc || die
- for i in ${pydocs}; do
- dosym /usr/share/doc/ccpn-data-${MY_MAJOR}/html/${i} ${in_path}/${i}
- done
-
- dosym /usr/share/ccpn/data ${in_path}/data
- dosym /usr/share/ccpn/model ${in_path}/model
-
- einfo "Adjusting permissions"
-
- files="
- cambridge/c/BayesPeakSeparator.so
- ccp/c/StructUtil.so
- ccp/c/StructStructure.so
- ccp/c/StructBond.so
- ccp/c/StructAtom.so
- ccpnmr/c/DyAtomCoord.so
- ccpnmr/c/DyDistConstraint.so
- ccpnmr/c/DyDistForce.so
- ccpnmr/c/AtomCoordList.so
- ccpnmr/c/DyAtomCoordList.so
- ccpnmr/c/ContourStyle.so
- ccpnmr/c/ContourLevels.so
- ccpnmr/c/SliceFile.so
- ccpnmr/c/PeakCluster.so
- ccpnmr/c/Dynamics.so
- ccpnmr/c/Bacus.so
- ccpnmr/c/Midge.so
- ccpnmr/c/DyDistConstraintList.so
- ccpnmr/c/WinPeakList.so
- ccpnmr/c/PeakList.so
- ccpnmr/c/DistConstraint.so
- ccpnmr/c/CloudUtil.so
- ccpnmr/c/DistForce.so
- ccpnmr/c/DistConstraintList.so
- ccpnmr/c/AtomCoord.so
- ccpnmr/c/DyDynamics.so
- ccpnmr/c/ContourFile.so
- memops/c/ShapeFile.so
- memops/c/BlockFile.so
- memops/c/PdfHandler.so
- memops/c/MemCache.so
- memops/c/FitMethod.so
- memops/c/PsHandler.so
- memops/c/GlHandler.so
- memops/c/StoreFile.so
- memops/c/StoreHandler.so
- memops/c/TkHandler.so"
- for FILE in ${files}; do
- fperms 755 ${in_path}/python/${FILE}
- done
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p110629.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p110629.ebuild
deleted file mode 100644
index cc3b7fd65f68..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.1.5_p110629.ebuild
+++ /dev/null
@@ -1,213 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p110629.ebuild,v 1.2 2011/10/07 19:29:31 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-PYTHON_USE_WITH="ssl tk"
-
-inherit eutils portability python toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
- [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.bz2"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="extendnmr +opengl"
-
-RDEPEND="
- dev-lang/tk[threads]
- >=dev-python/numpy-1.4
- >=dev-tcltk/tix-8.4.3
- =sci-libs/ccpn-data-"${MY_MAJOR}"*
- x11-libs/libXext
- x11-libs/libX11
- opengl? (
- media-libs/freeglut
- dev-python/pyglet )"
-# We need to fix this
-# sci-chemistry/mdd
-DEPEND="${RDEPEND}"
-PDEPEND="
- extendnmr? (
- <=sci-chemistry/aria-2.3.2
- sci-chemistry/prodecomp )"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
- epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
- local tk_ver
- local myconf
-
- tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
- if use opengl; then
- GLUT_NEED_INIT="-DNEED_GLUT_INIT"
- IGNORE_GL_FLAG=""
- GL_FLAG="-DUSE_GL_TRUE"
- GL_DIR="${EPREFIX}/usr"
- GL_LIB="-lglut -lGLU -lGL"
- GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
- GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
- else
- IGNORE_GL_FLAG="-DIGNORE_GL"
- GL_FLAG="-DUSE_GL_FALSE"
- fi
-
- GLUT_NOT_IN_GL=""
- GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
- rm -rf data model doc license || die
-
- sed \
- -e "s|/usr|${EPREFIX}/usr|g" \
- -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
- -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
- -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
- -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
- -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
- -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
- -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
- -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
- -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
- -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
- -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
- -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
- -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
- c/environment_default.txt > c/environment.txt
-}
-
-src_compile() {
- emake -C c all links || die
-}
-
-src_install() {
- local libdir
- local tkver
- local _wrapper
-
- find . -name "*.pyc" -type d -delete
-
- libdir=$(get_libdir)
- tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
- _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara"
- use extendnmr && _wrapper="${_wrapper} extendNmr"
- for wrapper in ${_wrapper}; do
- sed \
- -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
- -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
- -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
- -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
- -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
- -e "s|//|/|g" \
- "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
- dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
- done
-
- local in_path
- local files
- local pydocs
-
- pydocs="$(find python -name doc -type d)"
- rm -rf ${pydocs} || die
-
- in_path=$(python_get_sitedir)/${PN}
-
- for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
- sed \
- -e 's|#from __future__|from __future__|g' \
- -i ${i} || die
- done
-
- insinto ${in_path}
-
- dodir ${in_path}/c
-
- ebegin "Installing main files"
- doins -r python || die "main files installation failed"
- eend
- dosym ../../../..//share/doc/ccpn-data-${MY_MAJOR}/html ${in_path}/doc || die
- for i in ${pydocs}; do
- dosym /usr/share/doc/ccpn-data-${MY_MAJOR}/html/${i} ${in_path}/${i}
- done
-
- dosym /usr/share/ccpn/data ${in_path}/data
- dosym /usr/share/ccpn/model ${in_path}/model
-
- einfo "Adjusting permissions"
-
- files="
- cambridge/c/BayesPeakSeparator.so
- ccp/c/StructUtil.so
- ccp/c/StructStructure.so
- ccp/c/StructBond.so
- ccp/c/StructAtom.so
- ccpnmr/c/DyAtomCoord.so
- ccpnmr/c/DyDistConstraint.so
- ccpnmr/c/DyDistForce.so
- ccpnmr/c/AtomCoordList.so
- ccpnmr/c/DyAtomCoordList.so
- ccpnmr/c/ContourStyle.so
- ccpnmr/c/ContourLevels.so
- ccpnmr/c/SliceFile.so
- ccpnmr/c/PeakCluster.so
- ccpnmr/c/Dynamics.so
- ccpnmr/c/Bacus.so
- ccpnmr/c/Midge.so
- ccpnmr/c/DyDistConstraintList.so
- ccpnmr/c/WinPeakList.so
- ccpnmr/c/PeakList.so
- ccpnmr/c/DistConstraint.so
- ccpnmr/c/CloudUtil.so
- ccpnmr/c/DistForce.so
- ccpnmr/c/DistConstraintList.so
- ccpnmr/c/AtomCoord.so
- ccpnmr/c/DyDynamics.so
- ccpnmr/c/ContourFile.so
- memops/c/ShapeFile.so
- memops/c/BlockFile.so
- memops/c/PdfHandler.so
- memops/c/MemCache.so
- memops/c/FitMethod.so
- memops/c/PsHandler.so
- memops/c/GlHandler.so
- memops/c/StoreFile.so
- memops/c/StoreHandler.so
- memops/c/TkHandler.so"
- for FILE in ${files}; do
- fperms 755 ${in_path}/python/${FILE}
- done
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p110817.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p110817.ebuild
deleted file mode 100644
index 59cf2d672f31..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.1.5_p110817.ebuild
+++ /dev/null
@@ -1,213 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p110817.ebuild,v 1.2 2011/10/07 19:29:31 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-PYTHON_USE_WITH="ssl tk"
-
-inherit eutils portability python toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
- [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.bz2"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="extendnmr +opengl"
-
-RDEPEND="
- dev-lang/tk[threads]
- >=dev-python/numpy-1.4
- >=dev-tcltk/tix-8.4.3
- =sci-libs/ccpn-data-"${MY_MAJOR}"*
- x11-libs/libXext
- x11-libs/libX11
- opengl? (
- media-libs/freeglut
- dev-python/pyglet )"
-# We need to fix this
-# sci-chemistry/mdd
-DEPEND="${RDEPEND}"
-PDEPEND="
- extendnmr? (
- <=sci-chemistry/aria-2.3.2
- sci-chemistry/prodecomp )"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
- epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
- local tk_ver
- local myconf
-
- tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
- if use opengl; then
- GLUT_NEED_INIT="-DNEED_GLUT_INIT"
- IGNORE_GL_FLAG=""
- GL_FLAG="-DUSE_GL_TRUE"
- GL_DIR="${EPREFIX}/usr"
- GL_LIB="-lglut -lGLU -lGL"
- GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
- GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
- else
- IGNORE_GL_FLAG="-DIGNORE_GL"
- GL_FLAG="-DUSE_GL_FALSE"
- fi
-
- GLUT_NOT_IN_GL=""
- GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
- rm -rf data model doc license || die
-
- sed \
- -e "s|/usr|${EPREFIX}/usr|g" \
- -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
- -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
- -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
- -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
- -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
- -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
- -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
- -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
- -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
- -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
- -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
- -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
- -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
- c/environment_default.txt > c/environment.txt
-}
-
-src_compile() {
- emake -C c all links || die
-}
-
-src_install() {
- local libdir
- local tkver
- local _wrapper
-
- find . -name "*.pyc" -type d -delete
-
- libdir=$(get_libdir)
- tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
- _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara"
- use extendnmr && _wrapper="${_wrapper} extendNmr"
- for wrapper in ${_wrapper}; do
- sed \
- -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
- -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
- -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
- -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
- -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
- -e "s|//|/|g" \
- "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
- dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
- done
-
- local in_path
- local files
- local pydocs
-
- pydocs="$(find python -name doc -type d)"
- rm -rf ${pydocs} || die
-
- in_path=$(python_get_sitedir)/${PN}
-
- for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
- sed \
- -e 's|#from __future__|from __future__|g' \
- -i ${i} || die
- done
-
- insinto ${in_path}
-
- dodir ${in_path}/c
-
- ebegin "Installing main files"
- doins -r python || die "main files installation failed"
- eend
- dosym ../../../..//share/doc/ccpn-data-${MY_MAJOR}/html ${in_path}/doc || die
- for i in ${pydocs}; do
- dosym /usr/share/doc/ccpn-data-${MY_MAJOR}/html/${i} ${in_path}/${i}
- done
-
- dosym /usr/share/ccpn/data ${in_path}/data
- dosym /usr/share/ccpn/model ${in_path}/model
-
- einfo "Adjusting permissions"
-
- files="
- cambridge/c/BayesPeakSeparator.so
- ccp/c/StructUtil.so
- ccp/c/StructStructure.so
- ccp/c/StructBond.so
- ccp/c/StructAtom.so
- ccpnmr/c/DyAtomCoord.so
- ccpnmr/c/DyDistConstraint.so
- ccpnmr/c/DyDistForce.so
- ccpnmr/c/AtomCoordList.so
- ccpnmr/c/DyAtomCoordList.so
- ccpnmr/c/ContourStyle.so
- ccpnmr/c/ContourLevels.so
- ccpnmr/c/SliceFile.so
- ccpnmr/c/PeakCluster.so
- ccpnmr/c/Dynamics.so
- ccpnmr/c/Bacus.so
- ccpnmr/c/Midge.so
- ccpnmr/c/DyDistConstraintList.so
- ccpnmr/c/WinPeakList.so
- ccpnmr/c/PeakList.so
- ccpnmr/c/DistConstraint.so
- ccpnmr/c/CloudUtil.so
- ccpnmr/c/DistForce.so
- ccpnmr/c/DistConstraintList.so
- ccpnmr/c/AtomCoord.so
- ccpnmr/c/DyDynamics.so
- ccpnmr/c/ContourFile.so
- memops/c/ShapeFile.so
- memops/c/BlockFile.so
- memops/c/PdfHandler.so
- memops/c/MemCache.so
- memops/c/FitMethod.so
- memops/c/PsHandler.so
- memops/c/GlHandler.so
- memops/c/StoreFile.so
- memops/c/StoreHandler.so
- memops/c/TkHandler.so"
- for FILE in ${files}; do
- fperms 755 ${in_path}/python/${FILE}
- done
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p110905.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p110905.ebuild
deleted file mode 100644
index 312267b7a9d2..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.1.5_p110905.ebuild
+++ /dev/null
@@ -1,213 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p110905.ebuild,v 1.2 2011/10/07 19:29:31 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-PYTHON_USE_WITH="ssl tk"
-
-inherit eutils portability python toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
- [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.bz2"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="extendnmr +opengl"
-
-RDEPEND="
- dev-lang/tk[threads]
- >=dev-python/numpy-1.4
- >=dev-tcltk/tix-8.4.3
- =sci-libs/ccpn-data-"${MY_MAJOR}"*
- x11-libs/libXext
- x11-libs/libX11
- opengl? (
- media-libs/freeglut
- dev-python/pyglet )"
-# We need to fix this
-# sci-chemistry/mdd
-DEPEND="${RDEPEND}"
-PDEPEND="
- extendnmr? (
- <=sci-chemistry/aria-2.3.2
- sci-chemistry/prodecomp )"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
- epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
- local tk_ver
- local myconf
-
- tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
- if use opengl; then
- GLUT_NEED_INIT="-DNEED_GLUT_INIT"
- IGNORE_GL_FLAG=""
- GL_FLAG="-DUSE_GL_TRUE"
- GL_DIR="${EPREFIX}/usr"
- GL_LIB="-lglut -lGLU -lGL"
- GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
- GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
- else
- IGNORE_GL_FLAG="-DIGNORE_GL"
- GL_FLAG="-DUSE_GL_FALSE"
- fi
-
- GLUT_NOT_IN_GL=""
- GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
- rm -rf data model doc license || die
-
- sed \
- -e "s|/usr|${EPREFIX}/usr|g" \
- -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
- -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
- -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
- -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
- -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
- -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
- -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
- -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
- -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
- -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
- -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
- -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
- -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
- c/environment_default.txt > c/environment.txt
-}
-
-src_compile() {
- emake -C c all links || die
-}
-
-src_install() {
- local libdir
- local tkver
- local _wrapper
-
- find . -name "*.pyc" -type d -delete
-
- libdir=$(get_libdir)
- tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
- _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara"
- use extendnmr && _wrapper="${_wrapper} extendNmr"
- for wrapper in ${_wrapper}; do
- sed \
- -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
- -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
- -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
- -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
- -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
- -e "s|//|/|g" \
- "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
- dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
- done
-
- local in_path
- local files
- local pydocs
-
- pydocs="$(find python -name doc -type d)"
- rm -rf ${pydocs} || die
-
- in_path=$(python_get_sitedir)/${PN}
-
- for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
- sed \
- -e 's|#from __future__|from __future__|g' \
- -i ${i} || die
- done
-
- insinto ${in_path}
-
- dodir ${in_path}/c
-
- ebegin "Installing main files"
- doins -r python || die "main files installation failed"
- eend
- dosym ../../../..//share/doc/ccpn-data-${MY_MAJOR}/html ${in_path}/doc || die
- for i in ${pydocs}; do
- dosym /usr/share/doc/ccpn-data-${MY_MAJOR}/html/${i} ${in_path}/${i}
- done
-
- dosym /usr/share/ccpn/data ${in_path}/data
- dosym /usr/share/ccpn/model ${in_path}/model
-
- einfo "Adjusting permissions"
-
- files="
- cambridge/c/BayesPeakSeparator.so
- ccp/c/StructUtil.so
- ccp/c/StructStructure.so
- ccp/c/StructBond.so
- ccp/c/StructAtom.so
- ccpnmr/c/DyAtomCoord.so
- ccpnmr/c/DyDistConstraint.so
- ccpnmr/c/DyDistForce.so
- ccpnmr/c/AtomCoordList.so
- ccpnmr/c/DyAtomCoordList.so
- ccpnmr/c/ContourStyle.so
- ccpnmr/c/ContourLevels.so
- ccpnmr/c/SliceFile.so
- ccpnmr/c/PeakCluster.so
- ccpnmr/c/Dynamics.so
- ccpnmr/c/Bacus.so
- ccpnmr/c/Midge.so
- ccpnmr/c/DyDistConstraintList.so
- ccpnmr/c/WinPeakList.so
- ccpnmr/c/PeakList.so
- ccpnmr/c/DistConstraint.so
- ccpnmr/c/CloudUtil.so
- ccpnmr/c/DistForce.so
- ccpnmr/c/DistConstraintList.so
- ccpnmr/c/AtomCoord.so
- ccpnmr/c/DyDynamics.so
- ccpnmr/c/ContourFile.so
- memops/c/ShapeFile.so
- memops/c/BlockFile.so
- memops/c/PdfHandler.so
- memops/c/MemCache.so
- memops/c/FitMethod.so
- memops/c/PsHandler.so
- memops/c/GlHandler.so
- memops/c/StoreFile.so
- memops/c/StoreHandler.so
- memops/c/TkHandler.so"
- for FILE in ${files}; do
- fperms 755 ${in_path}/python/${FILE}
- done
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p110926.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p110926.ebuild
deleted file mode 100644
index 6a05a896dcbe..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.1.5_p110926.ebuild
+++ /dev/null
@@ -1,220 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p110926.ebuild,v 1.3 2011/10/19 07:25:58 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-PYTHON_USE_WITH="ssl tk"
-
-inherit eutils portability python toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
- [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.bz2"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="extendnmr +opengl"
-
-RDEPEND="
- dev-lang/tk[threads]
- >=dev-python/numpy-1.4
- >=dev-tcltk/tix-8.4.3
- =sci-libs/ccpn-data-"${MY_MAJOR}"*
- sci-biology/psipred
- x11-libs/libXext
- x11-libs/libX11
- opengl? (
- media-libs/freeglut
- dev-python/pyglet )"
-# We need to fix this
-# sci-chemistry/mdd
-DEPEND="${RDEPEND}"
-PDEPEND="
- extendnmr? (
- <=sci-chemistry/aria-2.3.2
- sci-chemistry/prodecomp )"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
- epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
- sed \
- -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
- -e "s:weights_s:weights:g" \
- -i python/ccpnmr/analysis/wrappers/Psipred.py || die
-
- local tk_ver
- local myconf
-
- tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
- if use opengl; then
- GLUT_NEED_INIT="-DNEED_GLUT_INIT"
- IGNORE_GL_FLAG=""
- GL_FLAG="-DUSE_GL_TRUE"
- GL_DIR="${EPREFIX}/usr"
- GL_LIB="-lglut -lGLU -lGL"
- GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
- GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
- else
- IGNORE_GL_FLAG="-DIGNORE_GL"
- GL_FLAG="-DUSE_GL_FALSE"
- fi
-
- GLUT_NOT_IN_GL=""
- GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
- rm -rf data model doc license || die
-
- sed \
- -e "s|/usr|${EPREFIX}/usr|g" \
- -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
- -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
- -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
- -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
- -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
- -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
- -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
- -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
- -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
- -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
- -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
- -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
- -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
- c/environment_default.txt > c/environment.txt
-}
-
-src_compile() {
- emake -C c all links || die
-}
-
-src_install() {
- local libdir
- local tkver
- local _wrapper
-
- find . -name "*.pyc" -type d -delete
-
- libdir=$(get_libdir)
- tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
- _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara"
- use extendnmr && _wrapper="${_wrapper} extendNmr"
- for wrapper in ${_wrapper}; do
- sed \
- -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
- -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
- -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
- -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
- -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
- -e "s|gentoousr|${EPREFIX}/usr|g" \
- -e "s|//|/|g" \
- "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
- dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
- done
-
- local in_path
- local files
- local pydocs
-
- pydocs="$(find python -name doc -type d)"
- rm -rf ${pydocs} || die
-
- in_path=$(python_get_sitedir)/${PN}
-
- for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
- sed \
- -e 's|#from __future__|from __future__|g' \
- -i ${i} || die
- done
-
- insinto ${in_path}
-
- dodir ${in_path}/c
-
- ebegin "Installing main files"
- doins -r python || die "main files installation failed"
- eend
- dosym ../../../..//share/doc/ccpn-data-${MY_MAJOR}/html ${in_path}/doc || die
- for i in ${pydocs}; do
- dosym /usr/share/doc/ccpn-data-${MY_MAJOR}/html/${i} ${in_path}/${i}
- done
-
- dosym /usr/share/ccpn/data ${in_path}/data
- dosym /usr/share/ccpn/model ${in_path}/model
-
- einfo "Adjusting permissions"
-
- files="
- cambridge/c/BayesPeakSeparator.so
- ccp/c/StructUtil.so
- ccp/c/StructStructure.so
- ccp/c/StructBond.so
- ccp/c/StructAtom.so
- ccpnmr/c/DyAtomCoord.so
- ccpnmr/c/DyDistConstraint.so
- ccpnmr/c/DyDistForce.so
- ccpnmr/c/AtomCoordList.so
- ccpnmr/c/DyAtomCoordList.so
- ccpnmr/c/ContourStyle.so
- ccpnmr/c/ContourLevels.so
- ccpnmr/c/SliceFile.so
- ccpnmr/c/PeakCluster.so
- ccpnmr/c/Dynamics.so
- ccpnmr/c/Bacus.so
- ccpnmr/c/Midge.so
- ccpnmr/c/DyDistConstraintList.so
- ccpnmr/c/WinPeakList.so
- ccpnmr/c/PeakList.so
- ccpnmr/c/DistConstraint.so
- ccpnmr/c/CloudUtil.so
- ccpnmr/c/DistForce.so
- ccpnmr/c/DistConstraintList.so
- ccpnmr/c/AtomCoord.so
- ccpnmr/c/DyDynamics.so
- ccpnmr/c/ContourFile.so
- memops/c/ShapeFile.so
- memops/c/BlockFile.so
- memops/c/PdfHandler.so
- memops/c/MemCache.so
- memops/c/FitMethod.so
- memops/c/PsHandler.so
- memops/c/GlHandler.so
- memops/c/StoreFile.so
- memops/c/StoreHandler.so
- memops/c/TkHandler.so"
- for FILE in ${files}; do
- fperms 755 ${in_path}/python/${FILE}
- done
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p111011.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p111011.ebuild
deleted file mode 100644
index bdb3bf68f7b6..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.1.5_p111011.ebuild
+++ /dev/null
@@ -1,214 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p111011.ebuild,v 1.2 2011/10/19 07:25:58 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-PYTHON_USE_WITH="ssl tk"
-
-inherit eutils portability python toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
- [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="extendnmr +opengl"
-
-RDEPEND="
- dev-lang/tk[threads]
- >=dev-python/numpy-1.4
- >=dev-tcltk/tix-8.4.3
- =sci-libs/ccpn-data-"${MY_MAJOR}"*
- >=sci-libs/ccpn-data-${PVR}
- sci-biology/psipred
- x11-libs/libXext
- x11-libs/libX11
- opengl? (
- media-libs/freeglut
- dev-python/pyglet )"
-# We need to fix this
-# sci-chemistry/mdd
-DEPEND="${RDEPEND}"
-PDEPEND="
- extendnmr? (
- <=sci-chemistry/aria-2.3.2
- sci-chemistry/prodecomp )"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
- epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
- sed \
- -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
- -e "s:weights_s:weights:g" \
- -i python/ccpnmr/analysis/wrappers/Psipred.py || die
-
- local tk_ver
- local myconf
-
- tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
- if use opengl; then
- GLUT_NEED_INIT="-DNEED_GLUT_INIT"
- IGNORE_GL_FLAG=""
- GL_FLAG="-DUSE_GL_TRUE"
- GL_DIR="${EPREFIX}/usr"
- GL_LIB="-lglut -lGLU -lGL"
- GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
- GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
- else
- IGNORE_GL_FLAG="-DIGNORE_GL"
- GL_FLAG="-DUSE_GL_FALSE"
- fi
-
- GLUT_NOT_IN_GL=""
- GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
- rm -rf data model doc license || die
-
- sed \
- -e "s|/usr|${EPREFIX}/usr|g" \
- -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
- -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
- -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
- -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
- -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
- -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
- -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
- -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
- -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
- -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
- -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
- -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
- -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
- c/environment_default.txt > c/environment.txt
-}
-
-src_compile() {
- emake -C c all links || die
-}
-
-src_install() {
- local libdir
- local tkver
- local _wrapper
-
- find . -name "*.pyc" -type d -delete
-
- libdir=$(get_libdir)
- tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
- _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara"
- use extendnmr && _wrapper="${_wrapper} extendNmr"
- for wrapper in ${_wrapper}; do
- sed \
- -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
- -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
- -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
- -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
- -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
- -e "s|gentoousr|${EPREFIX}/usr|g" \
- -e "s|//|/|g" \
- "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
- dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
- done
-
- local in_path
- local files
- local pydocs
-
- pydocs="$(find python -name doc -type d)"
- rm -rf ${pydocs} || die
-
- in_path=$(python_get_sitedir)/${PN}
-
- for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
- sed \
- -e 's|#from __future__|from __future__|g' \
- -i ${i} || die
- done
-
- insinto ${in_path}
-
- dodir ${in_path}/c
-
- ebegin "Installing main files"
- doins -r python || die "main files installation failed"
- eend
-
- einfo "Adjusting permissions"
-
- files="
- cambridge/c/BayesPeakSeparator.so
- ccp/c/StructUtil.so
- ccp/c/StructStructure.so
- ccp/c/StructBond.so
- ccp/c/StructAtom.so
- ccpnmr/c/DyAtomCoord.so
- ccpnmr/c/DyDistConstraint.so
- ccpnmr/c/DyDistForce.so
- ccpnmr/c/AtomCoordList.so
- ccpnmr/c/DyAtomCoordList.so
- ccpnmr/c/ContourStyle.so
- ccpnmr/c/ContourLevels.so
- ccpnmr/c/SliceFile.so
- ccpnmr/c/PeakCluster.so
- ccpnmr/c/Dynamics.so
- ccpnmr/c/Bacus.so
- ccpnmr/c/Midge.so
- ccpnmr/c/DyDistConstraintList.so
- ccpnmr/c/WinPeakList.so
- ccpnmr/c/PeakList.so
- ccpnmr/c/DistConstraint.so
- ccpnmr/c/CloudUtil.so
- ccpnmr/c/DistForce.so
- ccpnmr/c/DistConstraintList.so
- ccpnmr/c/AtomCoord.so
- ccpnmr/c/DyDynamics.so
- ccpnmr/c/ContourFile.so
- memops/c/ShapeFile.so
- memops/c/BlockFile.so
- memops/c/PdfHandler.so
- memops/c/MemCache.so
- memops/c/FitMethod.so
- memops/c/PsHandler.so
- memops/c/GlHandler.so
- memops/c/StoreFile.so
- memops/c/StoreHandler.so
- memops/c/TkHandler.so"
- for FILE in ${files}; do
- fperms 755 ${in_path}/python/${FILE}
- done
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p111017.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p111017.ebuild
deleted file mode 100644
index 6d841300e841..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.1.5_p111017.ebuild
+++ /dev/null
@@ -1,214 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p111017.ebuild,v 1.2 2011/10/19 07:25:58 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-PYTHON_USE_WITH="ssl tk"
-
-inherit eutils portability python toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
- [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="extendnmr +opengl"
-
-RDEPEND="
- dev-lang/tk[threads]
- >=dev-python/numpy-1.4
- >=dev-tcltk/tix-8.4.3
- =sci-libs/ccpn-data-"${MY_MAJOR}"*
- >=sci-libs/ccpn-data-2.1.5_p111011
- sci-biology/psipred
- x11-libs/libXext
- x11-libs/libX11
- opengl? (
- media-libs/freeglut
- dev-python/pyglet )"
-# We need to fix this
-# sci-chemistry/mdd
-DEPEND="${RDEPEND}"
-PDEPEND="
- extendnmr? (
- <=sci-chemistry/aria-2.3.2
- sci-chemistry/prodecomp )"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
- epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
- sed \
- -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
- -e "s:weights_s:weights:g" \
- -i python/ccpnmr/analysis/wrappers/Psipred.py || die
-
- local tk_ver
- local myconf
-
- tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
- if use opengl; then
- GLUT_NEED_INIT="-DNEED_GLUT_INIT"
- IGNORE_GL_FLAG=""
- GL_FLAG="-DUSE_GL_TRUE"
- GL_DIR="${EPREFIX}/usr"
- GL_LIB="-lglut -lGLU -lGL"
- GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
- GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
- else
- IGNORE_GL_FLAG="-DIGNORE_GL"
- GL_FLAG="-DUSE_GL_FALSE"
- fi
-
- GLUT_NOT_IN_GL=""
- GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
- rm -rf data model doc license || die
-
- sed \
- -e "s|/usr|${EPREFIX}/usr|g" \
- -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
- -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
- -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
- -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
- -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
- -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
- -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
- -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
- -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
- -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
- -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
- -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
- -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
- c/environment_default.txt > c/environment.txt
-}
-
-src_compile() {
- emake -C c all links || die
-}
-
-src_install() {
- local libdir
- local tkver
- local _wrapper
-
- find . -name "*.pyc" -type d -delete
-
- libdir=$(get_libdir)
- tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
- _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara"
- use extendnmr && _wrapper="${_wrapper} extendNmr"
- for wrapper in ${_wrapper}; do
- sed \
- -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
- -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
- -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
- -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
- -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
- -e "s|gentoousr|${EPREFIX}/usr|g" \
- -e "s|//|/|g" \
- "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
- dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
- done
-
- local in_path
- local files
- local pydocs
-
- pydocs="$(find python -name doc -type d)"
- rm -rf ${pydocs} || die
-
- in_path=$(python_get_sitedir)/${PN}
-
- for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
- sed \
- -e 's|#from __future__|from __future__|g' \
- -i ${i} || die
- done
-
- insinto ${in_path}
-
- dodir ${in_path}/c
-
- ebegin "Installing main files"
- doins -r python || die "main files installation failed"
- eend
-
- einfo "Adjusting permissions"
-
- files="
- cambridge/c/BayesPeakSeparator.so
- ccp/c/StructUtil.so
- ccp/c/StructStructure.so
- ccp/c/StructBond.so
- ccp/c/StructAtom.so
- ccpnmr/c/DyAtomCoord.so
- ccpnmr/c/DyDistConstraint.so
- ccpnmr/c/DyDistForce.so
- ccpnmr/c/AtomCoordList.so
- ccpnmr/c/DyAtomCoordList.so
- ccpnmr/c/ContourStyle.so
- ccpnmr/c/ContourLevels.so
- ccpnmr/c/SliceFile.so
- ccpnmr/c/PeakCluster.so
- ccpnmr/c/Dynamics.so
- ccpnmr/c/Bacus.so
- ccpnmr/c/Midge.so
- ccpnmr/c/DyDistConstraintList.so
- ccpnmr/c/WinPeakList.so
- ccpnmr/c/PeakList.so
- ccpnmr/c/DistConstraint.so
- ccpnmr/c/CloudUtil.so
- ccpnmr/c/DistForce.so
- ccpnmr/c/DistConstraintList.so
- ccpnmr/c/AtomCoord.so
- ccpnmr/c/DyDynamics.so
- ccpnmr/c/ContourFile.so
- memops/c/ShapeFile.so
- memops/c/BlockFile.so
- memops/c/PdfHandler.so
- memops/c/MemCache.so
- memops/c/FitMethod.so
- memops/c/PsHandler.so
- memops/c/GlHandler.so
- memops/c/StoreFile.so
- memops/c/StoreHandler.so
- memops/c/TkHandler.so"
- for FILE in ${files}; do
- fperms 755 ${in_path}/python/${FILE}
- done
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p111028.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p111028.ebuild
deleted file mode 100644
index 8d2ee4842c7c..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.1.5_p111028.ebuild
+++ /dev/null
@@ -1,214 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p111028.ebuild,v 1.1 2011/10/28 08:50:29 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-PYTHON_USE_WITH="ssl tk"
-
-inherit eutils portability python toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
- [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="extendnmr +opengl"
-
-RDEPEND="
- dev-lang/tk[threads]
- >=dev-python/numpy-1.4
- >=dev-tcltk/tix-8.4.3
- =sci-libs/ccpn-data-"${MY_MAJOR}"*
- >=sci-libs/ccpn-data-2.1.5_p111011
- sci-biology/psipred
- x11-libs/libXext
- x11-libs/libX11
- opengl? (
- media-libs/freeglut
- dev-python/pyglet )"
-# We need to fix this
-# sci-chemistry/mdd
-DEPEND="${RDEPEND}"
-PDEPEND="
- extendnmr? (
- <=sci-chemistry/aria-2.3.2
- sci-chemistry/prodecomp )"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
- epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
- sed \
- -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
- -e "s:weights_s:weights:g" \
- -i python/ccpnmr/analysis/wrappers/Psipred.py || die
-
- local tk_ver
- local myconf
-
- tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
- if use opengl; then
- GLUT_NEED_INIT="-DNEED_GLUT_INIT"
- IGNORE_GL_FLAG=""
- GL_FLAG="-DUSE_GL_TRUE"
- GL_DIR="${EPREFIX}/usr"
- GL_LIB="-lglut -lGLU -lGL"
- GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
- GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
- else
- IGNORE_GL_FLAG="-DIGNORE_GL"
- GL_FLAG="-DUSE_GL_FALSE"
- fi
-
- GLUT_NOT_IN_GL=""
- GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
- rm -rf data model doc license || die
-
- sed \
- -e "s|/usr|${EPREFIX}/usr|g" \
- -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
- -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
- -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
- -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
- -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
- -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
- -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
- -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
- -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
- -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
- -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
- -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
- -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
- c/environment_default.txt > c/environment.txt
-}
-
-src_compile() {
- emake -C c all links || die
-}
-
-src_install() {
- local libdir
- local tkver
- local _wrapper
-
- find . -name "*.pyc" -type d -delete
-
- libdir=$(get_libdir)
- tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
- _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara"
- use extendnmr && _wrapper="${_wrapper} extendNmr"
- for wrapper in ${_wrapper}; do
- sed \
- -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
- -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
- -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
- -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
- -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
- -e "s|gentoousr|${EPREFIX}/usr|g" \
- -e "s|//|/|g" \
- "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
- dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
- done
-
- local in_path
- local files
- local pydocs
-
- pydocs="$(find python -name doc -type d)"
- rm -rf ${pydocs} || die
-
- in_path=$(python_get_sitedir)/${PN}
-
- for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
- sed \
- -e 's|#from __future__|from __future__|g' \
- -i ${i} || die
- done
-
- insinto ${in_path}
-
- dodir ${in_path}/c
-
- ebegin "Installing main files"
- doins -r python || die "main files installation failed"
- eend
-
- einfo "Adjusting permissions"
-
- files="
- cambridge/c/BayesPeakSeparator.so
- ccp/c/StructUtil.so
- ccp/c/StructStructure.so
- ccp/c/StructBond.so
- ccp/c/StructAtom.so
- ccpnmr/c/DyAtomCoord.so
- ccpnmr/c/DyDistConstraint.so
- ccpnmr/c/DyDistForce.so
- ccpnmr/c/AtomCoordList.so
- ccpnmr/c/DyAtomCoordList.so
- ccpnmr/c/ContourStyle.so
- ccpnmr/c/ContourLevels.so
- ccpnmr/c/SliceFile.so
- ccpnmr/c/PeakCluster.so
- ccpnmr/c/Dynamics.so
- ccpnmr/c/Bacus.so
- ccpnmr/c/Midge.so
- ccpnmr/c/DyDistConstraintList.so
- ccpnmr/c/WinPeakList.so
- ccpnmr/c/PeakList.so
- ccpnmr/c/DistConstraint.so
- ccpnmr/c/CloudUtil.so
- ccpnmr/c/DistForce.so
- ccpnmr/c/DistConstraintList.so
- ccpnmr/c/AtomCoord.so
- ccpnmr/c/DyDynamics.so
- ccpnmr/c/ContourFile.so
- memops/c/ShapeFile.so
- memops/c/BlockFile.so
- memops/c/PdfHandler.so
- memops/c/MemCache.so
- memops/c/FitMethod.so
- memops/c/PsHandler.so
- memops/c/GlHandler.so
- memops/c/StoreFile.so
- memops/c/StoreHandler.so
- memops/c/TkHandler.so"
- for FILE in ${files}; do
- fperms 755 ${in_path}/python/${FILE}
- done
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.1.5_p111124.ebuild b/sci-chemistry/ccpn/ccpn-2.1.5_p111220.ebuild
index c1ecb9ceaede..1ae1679ac13f 100644
--- a/sci-chemistry/ccpn/ccpn-2.1.5_p111124.ebuild
+++ b/sci-chemistry/ccpn/ccpn-2.1.5_p111220.ebuild
@@ -1,6 +1,6 @@
# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p111124.ebuild,v 1.1 2011/11/24 08:36:43 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.1.5_p111220.ebuild,v 1.1 2011/12/20 08:39:39 jlec Exp $
EAPI="3"
diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p110602.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p110602.ebuild
deleted file mode 100644
index ed92da57f330..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.2.1_p110602.ebuild
+++ /dev/null
@@ -1,213 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p110602.ebuild,v 1.3 2011/10/07 19:29:31 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-PYTHON_USE_WITH="ssl tk"
-
-inherit eutils portability python toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
- [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.bz2"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="extendnmr +opengl"
-
-RDEPEND="
- dev-lang/tk[threads]
- >=dev-python/numpy-1.4
- >=dev-tcltk/tix-8.4.3
- =sci-libs/ccpn-data-"${MY_MAJOR}"*
- x11-libs/libXext
- x11-libs/libX11
- opengl? (
- media-libs/freeglut
- dev-python/pyglet )"
-# We need to fix this
-# sci-chemistry/mdd
-DEPEND="${RDEPEND}"
-PDEPEND="
- extendnmr? (
- >=sci-chemistry/aria-2.3.2-r1
- sci-chemistry/prodecomp )"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
- epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
- local tk_ver
- local myconf
-
- tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
- if use opengl; then
- GLUT_NEED_INIT="-DNEED_GLUT_INIT"
- IGNORE_GL_FLAG=""
- GL_FLAG="-DUSE_GL_TRUE"
- GL_DIR="${EPREFIX}/usr"
- GL_LIB="-lglut -lGLU -lGL"
- GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
- GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
- else
- IGNORE_GL_FLAG="-DIGNORE_GL"
- GL_FLAG="-DUSE_GL_FALSE"
- fi
-
- GLUT_NOT_IN_GL=""
- GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
- rm -rf data model doc license || die
-
- sed \
- -e "s|/usr|${EPREFIX}/usr|g" \
- -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
- -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
- -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
- -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
- -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
- -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
- -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
- -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
- -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
- -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
- -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
- -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
- -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
- c/environment_default.txt > c/environment.txt
-}
-
-src_compile() {
- emake -C c all links || die
-}
-
-src_install() {
- local libdir
- local tkver
- local _wrapper
-
- find . -name "*.pyc" -type d -delete
-
- libdir=$(get_libdir)
- tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
- _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara"
- use extendnmr && _wrapper="${_wrapper} extendNmr"
- for wrapper in ${_wrapper}; do
- sed \
- -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
- -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
- -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
- -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
- -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
- -e "s|//|/|g" \
- "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
- dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
- done
-
- local in_path
- local files
- local pydocs
-
- pydocs="$(find python -name doc -type d)"
- rm -rf ${pydocs} || die
-
- in_path=$(python_get_sitedir)/${PN}
-
- for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
- sed \
- -e 's|#from __future__|from __future__|g' \
- -i ${i} || die
- done
-
- insinto ${in_path}
-
- dodir ${in_path}/c
-
- ebegin "Installing main files"
- doins -r python || die "main files installation failed"
- eend
- dosym ../../../..//share/doc/ccpn-data-${MY_MAJOR}/html ${in_path}/doc || die
- for i in ${pydocs}; do
- dosym /usr/share/doc/ccpn-data-${MY_MAJOR}/html/${i} ${in_path}/${i}
- done
-
- dosym /usr/share/ccpn/data ${in_path}/data
- dosym /usr/share/ccpn/model ${in_path}/model
-
- einfo "Adjusting permissions"
-
- files="
- cambridge/c/BayesPeakSeparator.so
- ccp/c/StructUtil.so
- ccp/c/StructStructure.so
- ccp/c/StructBond.so
- ccp/c/StructAtom.so
- ccpnmr/c/DyAtomCoord.so
- ccpnmr/c/DyDistConstraint.so
- ccpnmr/c/DyDistForce.so
- ccpnmr/c/AtomCoordList.so
- ccpnmr/c/DyAtomCoordList.so
- ccpnmr/c/ContourStyle.so
- ccpnmr/c/ContourLevels.so
- ccpnmr/c/SliceFile.so
- ccpnmr/c/PeakCluster.so
- ccpnmr/c/Dynamics.so
- ccpnmr/c/Bacus.so
- ccpnmr/c/Midge.so
- ccpnmr/c/DyDistConstraintList.so
- ccpnmr/c/WinPeakList.so
- ccpnmr/c/PeakList.so
- ccpnmr/c/DistConstraint.so
- ccpnmr/c/CloudUtil.so
- ccpnmr/c/DistForce.so
- ccpnmr/c/DistConstraintList.so
- ccpnmr/c/AtomCoord.so
- ccpnmr/c/DyDynamics.so
- ccpnmr/c/ContourFile.so
- memops/c/ShapeFile.so
- memops/c/BlockFile.so
- memops/c/PdfHandler.so
- memops/c/MemCache.so
- memops/c/FitMethod.so
- memops/c/PsHandler.so
- memops/c/GlHandler.so
- memops/c/StoreFile.so
- memops/c/StoreHandler.so
- memops/c/TkHandler.so"
- for FILE in ${files}; do
- fperms 755 ${in_path}/python/${FILE}
- done
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p110629.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p110629.ebuild
deleted file mode 100644
index 06b9f66d1ba4..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.2.1_p110629.ebuild
+++ /dev/null
@@ -1,213 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p110629.ebuild,v 1.2 2011/10/07 19:29:31 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-PYTHON_USE_WITH="ssl tk"
-
-inherit eutils portability python toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
- [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.bz2"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="extendnmr +opengl"
-
-RDEPEND="
- dev-lang/tk[threads]
- >=dev-python/numpy-1.4
- >=dev-tcltk/tix-8.4.3
- =sci-libs/ccpn-data-"${MY_MAJOR}"*
- x11-libs/libXext
- x11-libs/libX11
- opengl? (
- media-libs/freeglut
- dev-python/pyglet )"
-# We need to fix this
-# sci-chemistry/mdd
-DEPEND="${RDEPEND}"
-PDEPEND="
- extendnmr? (
- >=sci-chemistry/aria-2.3.2-r1
- sci-chemistry/prodecomp )"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
- epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
- local tk_ver
- local myconf
-
- tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
- if use opengl; then
- GLUT_NEED_INIT="-DNEED_GLUT_INIT"
- IGNORE_GL_FLAG=""
- GL_FLAG="-DUSE_GL_TRUE"
- GL_DIR="${EPREFIX}/usr"
- GL_LIB="-lglut -lGLU -lGL"
- GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
- GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
- else
- IGNORE_GL_FLAG="-DIGNORE_GL"
- GL_FLAG="-DUSE_GL_FALSE"
- fi
-
- GLUT_NOT_IN_GL=""
- GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
- rm -rf data model doc license || die
-
- sed \
- -e "s|/usr|${EPREFIX}/usr|g" \
- -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
- -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
- -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
- -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
- -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
- -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
- -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
- -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
- -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
- -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
- -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
- -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
- -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
- c/environment_default.txt > c/environment.txt
-}
-
-src_compile() {
- emake -C c all links || die
-}
-
-src_install() {
- local libdir
- local tkver
- local _wrapper
-
- find . -name "*.pyc" -type d -delete
-
- libdir=$(get_libdir)
- tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
- _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara"
- use extendnmr && _wrapper="${_wrapper} extendNmr"
- for wrapper in ${_wrapper}; do
- sed \
- -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
- -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
- -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
- -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
- -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
- -e "s|//|/|g" \
- "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
- dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
- done
-
- local in_path
- local files
- local pydocs
-
- pydocs="$(find python -name doc -type d)"
- rm -rf ${pydocs} || die
-
- in_path=$(python_get_sitedir)/${PN}
-
- for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
- sed \
- -e 's|#from __future__|from __future__|g' \
- -i ${i} || die
- done
-
- insinto ${in_path}
-
- dodir ${in_path}/c
-
- ebegin "Installing main files"
- doins -r python || die "main files installation failed"
- eend
- dosym ../../../..//share/doc/ccpn-data-${MY_MAJOR}/html ${in_path}/doc || die
- for i in ${pydocs}; do
- dosym /usr/share/doc/ccpn-data-${MY_MAJOR}/html/${i} ${in_path}/${i}
- done
-
- dosym /usr/share/ccpn/data ${in_path}/data
- dosym /usr/share/ccpn/model ${in_path}/model
-
- einfo "Adjusting permissions"
-
- files="
- cambridge/c/BayesPeakSeparator.so
- ccp/c/StructUtil.so
- ccp/c/StructStructure.so
- ccp/c/StructBond.so
- ccp/c/StructAtom.so
- ccpnmr/c/DyAtomCoord.so
- ccpnmr/c/DyDistConstraint.so
- ccpnmr/c/DyDistForce.so
- ccpnmr/c/AtomCoordList.so
- ccpnmr/c/DyAtomCoordList.so
- ccpnmr/c/ContourStyle.so
- ccpnmr/c/ContourLevels.so
- ccpnmr/c/SliceFile.so
- ccpnmr/c/PeakCluster.so
- ccpnmr/c/Dynamics.so
- ccpnmr/c/Bacus.so
- ccpnmr/c/Midge.so
- ccpnmr/c/DyDistConstraintList.so
- ccpnmr/c/WinPeakList.so
- ccpnmr/c/PeakList.so
- ccpnmr/c/DistConstraint.so
- ccpnmr/c/CloudUtil.so
- ccpnmr/c/DistForce.so
- ccpnmr/c/DistConstraintList.so
- ccpnmr/c/AtomCoord.so
- ccpnmr/c/DyDynamics.so
- ccpnmr/c/ContourFile.so
- memops/c/ShapeFile.so
- memops/c/BlockFile.so
- memops/c/PdfHandler.so
- memops/c/MemCache.so
- memops/c/FitMethod.so
- memops/c/PsHandler.so
- memops/c/GlHandler.so
- memops/c/StoreFile.so
- memops/c/StoreHandler.so
- memops/c/TkHandler.so"
- for FILE in ${files}; do
- fperms 755 ${in_path}/python/${FILE}
- done
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p110817.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p110817.ebuild
deleted file mode 100644
index bb0a5d8b74e3..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.2.1_p110817.ebuild
+++ /dev/null
@@ -1,213 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p110817.ebuild,v 1.2 2011/10/07 19:29:31 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-PYTHON_USE_WITH="ssl tk"
-
-inherit eutils portability python toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
- [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.bz2"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="extendnmr +opengl"
-
-RDEPEND="
- dev-lang/tk[threads]
- >=dev-python/numpy-1.4
- >=dev-tcltk/tix-8.4.3
- =sci-libs/ccpn-data-"${MY_MAJOR}"*
- x11-libs/libXext
- x11-libs/libX11
- opengl? (
- media-libs/freeglut
- dev-python/pyglet )"
-# We need to fix this
-# sci-chemistry/mdd
-DEPEND="${RDEPEND}"
-PDEPEND="
- extendnmr? (
- >=sci-chemistry/aria-2.3.2-r1
- sci-chemistry/prodecomp )"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
- epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
- local tk_ver
- local myconf
-
- tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
- if use opengl; then
- GLUT_NEED_INIT="-DNEED_GLUT_INIT"
- IGNORE_GL_FLAG=""
- GL_FLAG="-DUSE_GL_TRUE"
- GL_DIR="${EPREFIX}/usr"
- GL_LIB="-lglut -lGLU -lGL"
- GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
- GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
- else
- IGNORE_GL_FLAG="-DIGNORE_GL"
- GL_FLAG="-DUSE_GL_FALSE"
- fi
-
- GLUT_NOT_IN_GL=""
- GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
- rm -rf data model doc license || die
-
- sed \
- -e "s|/usr|${EPREFIX}/usr|g" \
- -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
- -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
- -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
- -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
- -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
- -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
- -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
- -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
- -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
- -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
- -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
- -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
- -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
- c/environment_default.txt > c/environment.txt
-}
-
-src_compile() {
- emake -C c all links || die
-}
-
-src_install() {
- local libdir
- local tkver
- local _wrapper
-
- find . -name "*.pyc" -type d -delete
-
- libdir=$(get_libdir)
- tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
- _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara"
- use extendnmr && _wrapper="${_wrapper} extendNmr"
- for wrapper in ${_wrapper}; do
- sed \
- -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
- -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
- -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
- -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
- -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
- -e "s|//|/|g" \
- "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
- dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
- done
-
- local in_path
- local files
- local pydocs
-
- pydocs="$(find python -name doc -type d)"
- rm -rf ${pydocs} || die
-
- in_path=$(python_get_sitedir)/${PN}
-
- for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
- sed \
- -e 's|#from __future__|from __future__|g' \
- -i ${i} || die
- done
-
- insinto ${in_path}
-
- dodir ${in_path}/c
-
- ebegin "Installing main files"
- doins -r python || die "main files installation failed"
- eend
- dosym ../../../..//share/doc/ccpn-data-${MY_MAJOR}/html ${in_path}/doc || die
- for i in ${pydocs}; do
- dosym /usr/share/doc/ccpn-data-${MY_MAJOR}/html/${i} ${in_path}/${i}
- done
-
- dosym /usr/share/ccpn/data ${in_path}/data
- dosym /usr/share/ccpn/model ${in_path}/model
-
- einfo "Adjusting permissions"
-
- files="
- cambridge/c/BayesPeakSeparator.so
- ccp/c/StructUtil.so
- ccp/c/StructStructure.so
- ccp/c/StructBond.so
- ccp/c/StructAtom.so
- ccpnmr/c/DyAtomCoord.so
- ccpnmr/c/DyDistConstraint.so
- ccpnmr/c/DyDistForce.so
- ccpnmr/c/AtomCoordList.so
- ccpnmr/c/DyAtomCoordList.so
- ccpnmr/c/ContourStyle.so
- ccpnmr/c/ContourLevels.so
- ccpnmr/c/SliceFile.so
- ccpnmr/c/PeakCluster.so
- ccpnmr/c/Dynamics.so
- ccpnmr/c/Bacus.so
- ccpnmr/c/Midge.so
- ccpnmr/c/DyDistConstraintList.so
- ccpnmr/c/WinPeakList.so
- ccpnmr/c/PeakList.so
- ccpnmr/c/DistConstraint.so
- ccpnmr/c/CloudUtil.so
- ccpnmr/c/DistForce.so
- ccpnmr/c/DistConstraintList.so
- ccpnmr/c/AtomCoord.so
- ccpnmr/c/DyDynamics.so
- ccpnmr/c/ContourFile.so
- memops/c/ShapeFile.so
- memops/c/BlockFile.so
- memops/c/PdfHandler.so
- memops/c/MemCache.so
- memops/c/FitMethod.so
- memops/c/PsHandler.so
- memops/c/GlHandler.so
- memops/c/StoreFile.so
- memops/c/StoreHandler.so
- memops/c/TkHandler.so"
- for FILE in ${files}; do
- fperms 755 ${in_path}/python/${FILE}
- done
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p110905.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p110905.ebuild
deleted file mode 100644
index aa65d086692d..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.2.1_p110905.ebuild
+++ /dev/null
@@ -1,213 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p110905.ebuild,v 1.2 2011/10/07 19:29:31 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-PYTHON_USE_WITH="ssl tk"
-
-inherit eutils portability python toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
- [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.bz2"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="extendnmr +opengl"
-
-RDEPEND="
- dev-lang/tk[threads]
- >=dev-python/numpy-1.4
- >=dev-tcltk/tix-8.4.3
- =sci-libs/ccpn-data-"${MY_MAJOR}"*
- x11-libs/libXext
- x11-libs/libX11
- opengl? (
- media-libs/freeglut
- dev-python/pyglet )"
-# We need to fix this
-# sci-chemistry/mdd
-DEPEND="${RDEPEND}"
-PDEPEND="
- extendnmr? (
- >=sci-chemistry/aria-2.3.2-r1
- sci-chemistry/prodecomp )"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
- epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
- local tk_ver
- local myconf
-
- tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
- if use opengl; then
- GLUT_NEED_INIT="-DNEED_GLUT_INIT"
- IGNORE_GL_FLAG=""
- GL_FLAG="-DUSE_GL_TRUE"
- GL_DIR="${EPREFIX}/usr"
- GL_LIB="-lglut -lGLU -lGL"
- GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
- GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
- else
- IGNORE_GL_FLAG="-DIGNORE_GL"
- GL_FLAG="-DUSE_GL_FALSE"
- fi
-
- GLUT_NOT_IN_GL=""
- GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
- rm -rf data model doc license || die
-
- sed \
- -e "s|/usr|${EPREFIX}/usr|g" \
- -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
- -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
- -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
- -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
- -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
- -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
- -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
- -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
- -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
- -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
- -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
- -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
- -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
- c/environment_default.txt > c/environment.txt
-}
-
-src_compile() {
- emake -C c all links || die
-}
-
-src_install() {
- local libdir
- local tkver
- local _wrapper
-
- find . -name "*.pyc" -type d -delete
-
- libdir=$(get_libdir)
- tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
- _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara"
- use extendnmr && _wrapper="${_wrapper} extendNmr"
- for wrapper in ${_wrapper}; do
- sed \
- -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
- -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
- -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
- -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
- -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
- -e "s|//|/|g" \
- "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
- dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
- done
-
- local in_path
- local files
- local pydocs
-
- pydocs="$(find python -name doc -type d)"
- rm -rf ${pydocs} || die
-
- in_path=$(python_get_sitedir)/${PN}
-
- for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
- sed \
- -e 's|#from __future__|from __future__|g' \
- -i ${i} || die
- done
-
- insinto ${in_path}
-
- dodir ${in_path}/c
-
- ebegin "Installing main files"
- doins -r python || die "main files installation failed"
- eend
- dosym ../../../..//share/doc/ccpn-data-${MY_MAJOR}/html ${in_path}/doc || die
- for i in ${pydocs}; do
- dosym /usr/share/doc/ccpn-data-${MY_MAJOR}/html/${i} ${in_path}/${i}
- done
-
- dosym /usr/share/ccpn/data ${in_path}/data
- dosym /usr/share/ccpn/model ${in_path}/model
-
- einfo "Adjusting permissions"
-
- files="
- cambridge/c/BayesPeakSeparator.so
- ccp/c/StructUtil.so
- ccp/c/StructStructure.so
- ccp/c/StructBond.so
- ccp/c/StructAtom.so
- ccpnmr/c/DyAtomCoord.so
- ccpnmr/c/DyDistConstraint.so
- ccpnmr/c/DyDistForce.so
- ccpnmr/c/AtomCoordList.so
- ccpnmr/c/DyAtomCoordList.so
- ccpnmr/c/ContourStyle.so
- ccpnmr/c/ContourLevels.so
- ccpnmr/c/SliceFile.so
- ccpnmr/c/PeakCluster.so
- ccpnmr/c/Dynamics.so
- ccpnmr/c/Bacus.so
- ccpnmr/c/Midge.so
- ccpnmr/c/DyDistConstraintList.so
- ccpnmr/c/WinPeakList.so
- ccpnmr/c/PeakList.so
- ccpnmr/c/DistConstraint.so
- ccpnmr/c/CloudUtil.so
- ccpnmr/c/DistForce.so
- ccpnmr/c/DistConstraintList.so
- ccpnmr/c/AtomCoord.so
- ccpnmr/c/DyDynamics.so
- ccpnmr/c/ContourFile.so
- memops/c/ShapeFile.so
- memops/c/BlockFile.so
- memops/c/PdfHandler.so
- memops/c/MemCache.so
- memops/c/FitMethod.so
- memops/c/PsHandler.so
- memops/c/GlHandler.so
- memops/c/StoreFile.so
- memops/c/StoreHandler.so
- memops/c/TkHandler.so"
- for FILE in ${files}; do
- fperms 755 ${in_path}/python/${FILE}
- done
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p110926.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p110926.ebuild
deleted file mode 100644
index 81bba68c28b7..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.2.1_p110926.ebuild
+++ /dev/null
@@ -1,220 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p110926.ebuild,v 1.3 2011/10/19 07:25:58 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-PYTHON_USE_WITH="ssl tk"
-
-inherit eutils portability python toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
- [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.bz2"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="extendnmr +opengl"
-
-RDEPEND="
- dev-lang/tk[threads]
- >=dev-python/numpy-1.4
- >=dev-tcltk/tix-8.4.3
- =sci-libs/ccpn-data-"${MY_MAJOR}"*
- sci-biology/psipred
- x11-libs/libXext
- x11-libs/libX11
- opengl? (
- media-libs/freeglut
- dev-python/pyglet )"
-# We need to fix this
-# sci-chemistry/mdd
-DEPEND="${RDEPEND}"
-PDEPEND="
- extendnmr? (
- >=sci-chemistry/aria-2.3.2-r1
- sci-chemistry/prodecomp )"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
- epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
- sed \
- -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
- -e "s:weights_s:weights:g" \
- -i python/ccpnmr/analysis/wrappers/Psipred.py || die
-
- local tk_ver
- local myconf
-
- tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
- if use opengl; then
- GLUT_NEED_INIT="-DNEED_GLUT_INIT"
- IGNORE_GL_FLAG=""
- GL_FLAG="-DUSE_GL_TRUE"
- GL_DIR="${EPREFIX}/usr"
- GL_LIB="-lglut -lGLU -lGL"
- GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
- GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
- else
- IGNORE_GL_FLAG="-DIGNORE_GL"
- GL_FLAG="-DUSE_GL_FALSE"
- fi
-
- GLUT_NOT_IN_GL=""
- GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
- rm -rf data model doc license || die
-
- sed \
- -e "s|/usr|${EPREFIX}/usr|g" \
- -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
- -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
- -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
- -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
- -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
- -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
- -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
- -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
- -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
- -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
- -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
- -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
- -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
- c/environment_default.txt > c/environment.txt
-}
-
-src_compile() {
- emake -C c all links || die
-}
-
-src_install() {
- local libdir
- local tkver
- local _wrapper
-
- find . -name "*.pyc" -type d -delete
-
- libdir=$(get_libdir)
- tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
- _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara"
- use extendnmr && _wrapper="${_wrapper} extendNmr"
- for wrapper in ${_wrapper}; do
- sed \
- -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
- -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
- -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
- -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
- -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
- -e "s|gentoousr|${EPREFIX}/usr|g" \
- -e "s|//|/|g" \
- "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
- dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
- done
-
- local in_path
- local files
- local pydocs
-
- pydocs="$(find python -name doc -type d)"
- rm -rf ${pydocs} || die
-
- in_path=$(python_get_sitedir)/${PN}
-
- for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
- sed \
- -e 's|#from __future__|from __future__|g' \
- -i ${i} || die
- done
-
- insinto ${in_path}
-
- dodir ${in_path}/c
-
- ebegin "Installing main files"
- doins -r python || die "main files installation failed"
- eend
- dosym ../../../..//share/doc/ccpn-data-${MY_MAJOR}/html ${in_path}/doc || die
- for i in ${pydocs}; do
- dosym /usr/share/doc/ccpn-data-${MY_MAJOR}/html/${i} ${in_path}/${i}
- done
-
- dosym /usr/share/ccpn/data ${in_path}/data
- dosym /usr/share/ccpn/model ${in_path}/model
-
- einfo "Adjusting permissions"
-
- files="
- cambridge/c/BayesPeakSeparator.so
- ccp/c/StructUtil.so
- ccp/c/StructStructure.so
- ccp/c/StructBond.so
- ccp/c/StructAtom.so
- ccpnmr/c/DyAtomCoord.so
- ccpnmr/c/DyDistConstraint.so
- ccpnmr/c/DyDistForce.so
- ccpnmr/c/AtomCoordList.so
- ccpnmr/c/DyAtomCoordList.so
- ccpnmr/c/ContourStyle.so
- ccpnmr/c/ContourLevels.so
- ccpnmr/c/SliceFile.so
- ccpnmr/c/PeakCluster.so
- ccpnmr/c/Dynamics.so
- ccpnmr/c/Bacus.so
- ccpnmr/c/Midge.so
- ccpnmr/c/DyDistConstraintList.so
- ccpnmr/c/WinPeakList.so
- ccpnmr/c/PeakList.so
- ccpnmr/c/DistConstraint.so
- ccpnmr/c/CloudUtil.so
- ccpnmr/c/DistForce.so
- ccpnmr/c/DistConstraintList.so
- ccpnmr/c/AtomCoord.so
- ccpnmr/c/DyDynamics.so
- ccpnmr/c/ContourFile.so
- memops/c/ShapeFile.so
- memops/c/BlockFile.so
- memops/c/PdfHandler.so
- memops/c/MemCache.so
- memops/c/FitMethod.so
- memops/c/PsHandler.so
- memops/c/GlHandler.so
- memops/c/StoreFile.so
- memops/c/StoreHandler.so
- memops/c/TkHandler.so"
- for FILE in ${files}; do
- fperms 755 ${in_path}/python/${FILE}
- done
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p111011.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p111011.ebuild
deleted file mode 100644
index d0ae0c549ab9..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.2.1_p111011.ebuild
+++ /dev/null
@@ -1,214 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p111011.ebuild,v 1.2 2011/10/19 07:25:58 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-PYTHON_USE_WITH="ssl tk"
-
-inherit eutils portability python toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
- [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="extendnmr +opengl"
-
-RDEPEND="
- dev-lang/tk[threads]
- >=dev-python/numpy-1.4
- >=dev-tcltk/tix-8.4.3
- =sci-libs/ccpn-data-"${MY_MAJOR}"*
- >=sci-libs/ccpn-data-${PVR}
- sci-biology/psipred
- x11-libs/libXext
- x11-libs/libX11
- opengl? (
- media-libs/freeglut
- dev-python/pyglet )"
-# We need to fix this
-# sci-chemistry/mdd
-DEPEND="${RDEPEND}"
-PDEPEND="
- extendnmr? (
- >=sci-chemistry/aria-2.3.2-r1
- sci-chemistry/prodecomp )"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
- epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
- sed \
- -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
- -e "s:weights_s:weights:g" \
- -i python/ccpnmr/analysis/wrappers/Psipred.py || die
-
- local tk_ver
- local myconf
-
- tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
- if use opengl; then
- GLUT_NEED_INIT="-DNEED_GLUT_INIT"
- IGNORE_GL_FLAG=""
- GL_FLAG="-DUSE_GL_TRUE"
- GL_DIR="${EPREFIX}/usr"
- GL_LIB="-lglut -lGLU -lGL"
- GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
- GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
- else
- IGNORE_GL_FLAG="-DIGNORE_GL"
- GL_FLAG="-DUSE_GL_FALSE"
- fi
-
- GLUT_NOT_IN_GL=""
- GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
- rm -rf data model doc license || die
-
- sed \
- -e "s|/usr|${EPREFIX}/usr|g" \
- -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
- -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
- -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
- -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
- -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
- -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
- -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
- -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
- -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
- -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
- -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
- -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
- -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
- c/environment_default.txt > c/environment.txt
-}
-
-src_compile() {
- emake -C c all links || die
-}
-
-src_install() {
- local libdir
- local tkver
- local _wrapper
-
- find . -name "*.pyc" -type d -delete
-
- libdir=$(get_libdir)
- tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
- _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara"
- use extendnmr && _wrapper="${_wrapper} extendNmr"
- for wrapper in ${_wrapper}; do
- sed \
- -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
- -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
- -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
- -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
- -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
- -e "s|gentoousr|${EPREFIX}/usr|g" \
- -e "s|//|/|g" \
- "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
- dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
- done
-
- local in_path
- local files
- local pydocs
-
- pydocs="$(find python -name doc -type d)"
- rm -rf ${pydocs} || die
-
- in_path=$(python_get_sitedir)/${PN}
-
- for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
- sed \
- -e 's|#from __future__|from __future__|g' \
- -i ${i} || die
- done
-
- insinto ${in_path}
-
- dodir ${in_path}/c
-
- ebegin "Installing main files"
- doins -r python || die "main files installation failed"
- eend
-
- einfo "Adjusting permissions"
-
- files="
- cambridge/c/BayesPeakSeparator.so
- ccp/c/StructUtil.so
- ccp/c/StructStructure.so
- ccp/c/StructBond.so
- ccp/c/StructAtom.so
- ccpnmr/c/DyAtomCoord.so
- ccpnmr/c/DyDistConstraint.so
- ccpnmr/c/DyDistForce.so
- ccpnmr/c/AtomCoordList.so
- ccpnmr/c/DyAtomCoordList.so
- ccpnmr/c/ContourStyle.so
- ccpnmr/c/ContourLevels.so
- ccpnmr/c/SliceFile.so
- ccpnmr/c/PeakCluster.so
- ccpnmr/c/Dynamics.so
- ccpnmr/c/Bacus.so
- ccpnmr/c/Midge.so
- ccpnmr/c/DyDistConstraintList.so
- ccpnmr/c/WinPeakList.so
- ccpnmr/c/PeakList.so
- ccpnmr/c/DistConstraint.so
- ccpnmr/c/CloudUtil.so
- ccpnmr/c/DistForce.so
- ccpnmr/c/DistConstraintList.so
- ccpnmr/c/AtomCoord.so
- ccpnmr/c/DyDynamics.so
- ccpnmr/c/ContourFile.so
- memops/c/ShapeFile.so
- memops/c/BlockFile.so
- memops/c/PdfHandler.so
- memops/c/MemCache.so
- memops/c/FitMethod.so
- memops/c/PsHandler.so
- memops/c/GlHandler.so
- memops/c/StoreFile.so
- memops/c/StoreHandler.so
- memops/c/TkHandler.so"
- for FILE in ${files}; do
- fperms 755 ${in_path}/python/${FILE}
- done
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p111017.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p111017.ebuild
deleted file mode 100644
index e4f4f13a7c63..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.2.1_p111017.ebuild
+++ /dev/null
@@ -1,214 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p111017.ebuild,v 1.2 2011/10/19 07:25:58 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-PYTHON_USE_WITH="ssl tk"
-
-inherit eutils portability python toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
- [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="extendnmr +opengl"
-
-RDEPEND="
- dev-lang/tk[threads]
- >=dev-python/numpy-1.4
- >=dev-tcltk/tix-8.4.3
- =sci-libs/ccpn-data-"${MY_MAJOR}"*
- >=sci-libs/ccpn-data-2.2.1_p111011
- sci-biology/psipred
- x11-libs/libXext
- x11-libs/libX11
- opengl? (
- media-libs/freeglut
- dev-python/pyglet )"
-# We need to fix this
-# sci-chemistry/mdd
-DEPEND="${RDEPEND}"
-PDEPEND="
- extendnmr? (
- >=sci-chemistry/aria-2.3.2-r1
- sci-chemistry/prodecomp )"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
- epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
- sed \
- -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
- -e "s:weights_s:weights:g" \
- -i python/ccpnmr/analysis/wrappers/Psipred.py || die
-
- local tk_ver
- local myconf
-
- tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
- if use opengl; then
- GLUT_NEED_INIT="-DNEED_GLUT_INIT"
- IGNORE_GL_FLAG=""
- GL_FLAG="-DUSE_GL_TRUE"
- GL_DIR="${EPREFIX}/usr"
- GL_LIB="-lglut -lGLU -lGL"
- GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
- GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
- else
- IGNORE_GL_FLAG="-DIGNORE_GL"
- GL_FLAG="-DUSE_GL_FALSE"
- fi
-
- GLUT_NOT_IN_GL=""
- GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
- rm -rf data model doc license || die
-
- sed \
- -e "s|/usr|${EPREFIX}/usr|g" \
- -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
- -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
- -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
- -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
- -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
- -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
- -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
- -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
- -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
- -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
- -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
- -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
- -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
- c/environment_default.txt > c/environment.txt
-}
-
-src_compile() {
- emake -C c all links || die
-}
-
-src_install() {
- local libdir
- local tkver
- local _wrapper
-
- find . -name "*.pyc" -type d -delete
-
- libdir=$(get_libdir)
- tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
- _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara"
- use extendnmr && _wrapper="${_wrapper} extendNmr"
- for wrapper in ${_wrapper}; do
- sed \
- -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
- -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
- -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
- -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
- -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
- -e "s|gentoousr|${EPREFIX}/usr|g" \
- -e "s|//|/|g" \
- "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
- dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
- done
-
- local in_path
- local files
- local pydocs
-
- pydocs="$(find python -name doc -type d)"
- rm -rf ${pydocs} || die
-
- in_path=$(python_get_sitedir)/${PN}
-
- for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
- sed \
- -e 's|#from __future__|from __future__|g' \
- -i ${i} || die
- done
-
- insinto ${in_path}
-
- dodir ${in_path}/c
-
- ebegin "Installing main files"
- doins -r python || die "main files installation failed"
- eend
-
- einfo "Adjusting permissions"
-
- files="
- cambridge/c/BayesPeakSeparator.so
- ccp/c/StructUtil.so
- ccp/c/StructStructure.so
- ccp/c/StructBond.so
- ccp/c/StructAtom.so
- ccpnmr/c/DyAtomCoord.so
- ccpnmr/c/DyDistConstraint.so
- ccpnmr/c/DyDistForce.so
- ccpnmr/c/AtomCoordList.so
- ccpnmr/c/DyAtomCoordList.so
- ccpnmr/c/ContourStyle.so
- ccpnmr/c/ContourLevels.so
- ccpnmr/c/SliceFile.so
- ccpnmr/c/PeakCluster.so
- ccpnmr/c/Dynamics.so
- ccpnmr/c/Bacus.so
- ccpnmr/c/Midge.so
- ccpnmr/c/DyDistConstraintList.so
- ccpnmr/c/WinPeakList.so
- ccpnmr/c/PeakList.so
- ccpnmr/c/DistConstraint.so
- ccpnmr/c/CloudUtil.so
- ccpnmr/c/DistForce.so
- ccpnmr/c/DistConstraintList.so
- ccpnmr/c/AtomCoord.so
- ccpnmr/c/DyDynamics.so
- ccpnmr/c/ContourFile.so
- memops/c/ShapeFile.so
- memops/c/BlockFile.so
- memops/c/PdfHandler.so
- memops/c/MemCache.so
- memops/c/FitMethod.so
- memops/c/PsHandler.so
- memops/c/GlHandler.so
- memops/c/StoreFile.so
- memops/c/StoreHandler.so
- memops/c/TkHandler.so"
- for FILE in ${files}; do
- fperms 755 ${in_path}/python/${FILE}
- done
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p111019.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p111019.ebuild
deleted file mode 100644
index 51c99204e671..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.2.1_p111019.ebuild
+++ /dev/null
@@ -1,214 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p111019.ebuild,v 1.1 2011/10/19 07:25:58 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-PYTHON_USE_WITH="ssl tk"
-
-inherit eutils portability python toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
- [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="extendnmr +opengl"
-
-RDEPEND="
- dev-lang/tk[threads]
- >=dev-python/numpy-1.4
- >=dev-tcltk/tix-8.4.3
- =sci-libs/ccpn-data-"${MY_MAJOR}"*
- >=sci-libs/ccpn-data-2.2.1_p111011
- sci-biology/psipred
- x11-libs/libXext
- x11-libs/libX11
- opengl? (
- media-libs/freeglut
- dev-python/pyglet )"
-# We need to fix this
-# sci-chemistry/mdd
-DEPEND="${RDEPEND}"
-PDEPEND="
- extendnmr? (
- >=sci-chemistry/aria-2.3.2-r1
- sci-chemistry/prodecomp )"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
- epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
- sed \
- -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
- -e "s:weights_s:weights:g" \
- -i python/ccpnmr/analysis/wrappers/Psipred.py || die
-
- local tk_ver
- local myconf
-
- tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
- if use opengl; then
- GLUT_NEED_INIT="-DNEED_GLUT_INIT"
- IGNORE_GL_FLAG=""
- GL_FLAG="-DUSE_GL_TRUE"
- GL_DIR="${EPREFIX}/usr"
- GL_LIB="-lglut -lGLU -lGL"
- GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
- GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
- else
- IGNORE_GL_FLAG="-DIGNORE_GL"
- GL_FLAG="-DUSE_GL_FALSE"
- fi
-
- GLUT_NOT_IN_GL=""
- GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
- rm -rf data model doc license || die
-
- sed \
- -e "s|/usr|${EPREFIX}/usr|g" \
- -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
- -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
- -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
- -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
- -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
- -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
- -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
- -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
- -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
- -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
- -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
- -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
- -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
- c/environment_default.txt > c/environment.txt
-}
-
-src_compile() {
- emake -C c all links || die
-}
-
-src_install() {
- local libdir
- local tkver
- local _wrapper
-
- find . -name "*.pyc" -type d -delete
-
- libdir=$(get_libdir)
- tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
- _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara"
- use extendnmr && _wrapper="${_wrapper} extendNmr"
- for wrapper in ${_wrapper}; do
- sed \
- -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
- -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
- -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
- -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
- -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
- -e "s|gentoousr|${EPREFIX}/usr|g" \
- -e "s|//|/|g" \
- "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
- dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
- done
-
- local in_path
- local files
- local pydocs
-
- pydocs="$(find python -name doc -type d)"
- rm -rf ${pydocs} || die
-
- in_path=$(python_get_sitedir)/${PN}
-
- for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
- sed \
- -e 's|#from __future__|from __future__|g' \
- -i ${i} || die
- done
-
- insinto ${in_path}
-
- dodir ${in_path}/c
-
- ebegin "Installing main files"
- doins -r python || die "main files installation failed"
- eend
-
- einfo "Adjusting permissions"
-
- files="
- cambridge/c/BayesPeakSeparator.so
- ccp/c/StructUtil.so
- ccp/c/StructStructure.so
- ccp/c/StructBond.so
- ccp/c/StructAtom.so
- ccpnmr/c/DyAtomCoord.so
- ccpnmr/c/DyDistConstraint.so
- ccpnmr/c/DyDistForce.so
- ccpnmr/c/AtomCoordList.so
- ccpnmr/c/DyAtomCoordList.so
- ccpnmr/c/ContourStyle.so
- ccpnmr/c/ContourLevels.so
- ccpnmr/c/SliceFile.so
- ccpnmr/c/PeakCluster.so
- ccpnmr/c/Dynamics.so
- ccpnmr/c/Bacus.so
- ccpnmr/c/Midge.so
- ccpnmr/c/DyDistConstraintList.so
- ccpnmr/c/WinPeakList.so
- ccpnmr/c/PeakList.so
- ccpnmr/c/DistConstraint.so
- ccpnmr/c/CloudUtil.so
- ccpnmr/c/DistForce.so
- ccpnmr/c/DistConstraintList.so
- ccpnmr/c/AtomCoord.so
- ccpnmr/c/DyDynamics.so
- ccpnmr/c/ContourFile.so
- memops/c/ShapeFile.so
- memops/c/BlockFile.so
- memops/c/PdfHandler.so
- memops/c/MemCache.so
- memops/c/FitMethod.so
- memops/c/PsHandler.so
- memops/c/GlHandler.so
- memops/c/StoreFile.so
- memops/c/StoreHandler.so
- memops/c/TkHandler.so"
- for FILE in ${files}; do
- fperms 755 ${in_path}/python/${FILE}
- done
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p111028.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p111028.ebuild
deleted file mode 100644
index 479a8991247c..000000000000
--- a/sci-chemistry/ccpn/ccpn-2.2.1_p111028.ebuild
+++ /dev/null
@@ -1,214 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p111028.ebuild,v 1.1 2011/10/28 08:50:29 jlec Exp $
-
-EAPI="3"
-
-PYTHON_DEPEND="2:2.5"
-PYTHON_USE_WITH="ssl tk"
-
-inherit eutils portability python toolchain-funcs versionator
-
-PATCHSET="${PV##*_p}"
-MY_PN="${PN}mr"
-MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
-MY_MAJOR="$(get_version_component_range 1-3)"
-
-DESCRIPTION="The Collaborative Computing Project for NMR"
-SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
- [[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
-HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
-
-SLOT="0"
-LICENSE="|| ( CCPN LGPL-2.1 )"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="extendnmr +opengl"
-
-RDEPEND="
- dev-lang/tk[threads]
- >=dev-python/numpy-1.4
- >=dev-tcltk/tix-8.4.3
- =sci-libs/ccpn-data-"${MY_MAJOR}"*
- >=sci-libs/ccpn-data-2.2.1_p111011
- sci-biology/psipred
- x11-libs/libXext
- x11-libs/libX11
- opengl? (
- media-libs/freeglut
- dev-python/pyglet )"
-# We need to fix this
-# sci-chemistry/mdd
-DEPEND="${RDEPEND}"
-PDEPEND="
- extendnmr? (
- >=sci-chemistry/aria-2.3.2-r1
- sci-chemistry/prodecomp )"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
-
-pkg_setup() {
- python_set_active_version 2
-}
-
-src_prepare() {
- [[ -n ${PATCHSET} ]] && \
- epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
-
- epatch "${FILESDIR}"/${MY_PV}-parallel.patch
-
- sed \
- -e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
- -e "s:weights_s:weights:g" \
- -i python/ccpnmr/analysis/wrappers/Psipred.py || die
-
- local tk_ver
- local myconf
-
- tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
-
- if use opengl; then
- GLUT_NEED_INIT="-DNEED_GLUT_INIT"
- IGNORE_GL_FLAG=""
- GL_FLAG="-DUSE_GL_TRUE"
- GL_DIR="${EPREFIX}/usr"
- GL_LIB="-lglut -lGLU -lGL"
- GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
- GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
-
- else
- IGNORE_GL_FLAG="-DIGNORE_GL"
- GL_FLAG="-DUSE_GL_FALSE"
- fi
-
- GLUT_NOT_IN_GL=""
- GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
-
- rm -rf data model doc license || die
-
- sed \
- -e "s|/usr|${EPREFIX}/usr|g" \
- -e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
- -e "s|^\(OPT_FLAG =\).*|\1 ${CFLAGS}|g" \
- -e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
- -e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
- -e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
- -e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
- -e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
- -e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
- -e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
- -e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
- -e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
- -e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
- -e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I${EPREFIX}/$(python_get_includedir)|g" \
- -e "s|^\(PYTHON_LIB =\).*|\1 $(python_get_library -l)|g" \
- c/environment_default.txt > c/environment.txt
-}
-
-src_compile() {
- emake -C c all links || die
-}
-
-src_install() {
- local libdir
- local tkver
- local _wrapper
-
- find . -name "*.pyc" -type d -delete
-
- libdir=$(get_libdir)
- tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
-
- _wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara"
- use extendnmr && _wrapper="${_wrapper} extendNmr"
- for wrapper in ${_wrapper}; do
- sed \
- -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \
- -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
- -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
- -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
- -e "s|gentoopython|${EPREFIX}/usr/bin/python|g" \
- -e "s|gentoousr|${EPREFIX}/usr|g" \
- -e "s|//|/|g" \
- "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
- dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
- done
-
- local in_path
- local files
- local pydocs
-
- pydocs="$(find python -name doc -type d)"
- rm -rf ${pydocs} || die
-
- in_path=$(python_get_sitedir)/${PN}
-
- for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
- sed \
- -e 's|#from __future__|from __future__|g' \
- -i ${i} || die
- done
-
- insinto ${in_path}
-
- dodir ${in_path}/c
-
- ebegin "Installing main files"
- doins -r python || die "main files installation failed"
- eend
-
- einfo "Adjusting permissions"
-
- files="
- cambridge/c/BayesPeakSeparator.so
- ccp/c/StructUtil.so
- ccp/c/StructStructure.so
- ccp/c/StructBond.so
- ccp/c/StructAtom.so
- ccpnmr/c/DyAtomCoord.so
- ccpnmr/c/DyDistConstraint.so
- ccpnmr/c/DyDistForce.so
- ccpnmr/c/AtomCoordList.so
- ccpnmr/c/DyAtomCoordList.so
- ccpnmr/c/ContourStyle.so
- ccpnmr/c/ContourLevels.so
- ccpnmr/c/SliceFile.so
- ccpnmr/c/PeakCluster.so
- ccpnmr/c/Dynamics.so
- ccpnmr/c/Bacus.so
- ccpnmr/c/Midge.so
- ccpnmr/c/DyDistConstraintList.so
- ccpnmr/c/WinPeakList.so
- ccpnmr/c/PeakList.so
- ccpnmr/c/DistConstraint.so
- ccpnmr/c/CloudUtil.so
- ccpnmr/c/DistForce.so
- ccpnmr/c/DistConstraintList.so
- ccpnmr/c/AtomCoord.so
- ccpnmr/c/DyDynamics.so
- ccpnmr/c/ContourFile.so
- memops/c/ShapeFile.so
- memops/c/BlockFile.so
- memops/c/PdfHandler.so
- memops/c/MemCache.so
- memops/c/FitMethod.so
- memops/c/PsHandler.so
- memops/c/GlHandler.so
- memops/c/StoreFile.so
- memops/c/StoreHandler.so
- memops/c/TkHandler.so"
- for FILE in ${files}; do
- fperms 755 ${in_path}/python/${FILE}
- done
-}
-
-pkg_postinst() {
- python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
- python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/ccpn/ccpn-2.2.1_p111124.ebuild b/sci-chemistry/ccpn/ccpn-2.2.1_p111220.ebuild
index 14650a1952d9..e1600d68538f 100644
--- a/sci-chemistry/ccpn/ccpn-2.2.1_p111124.ebuild
+++ b/sci-chemistry/ccpn/ccpn-2.2.1_p111220.ebuild
@@ -1,6 +1,6 @@
# Copyright 1999-2011 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p111124.ebuild,v 1.1 2011/11/24 08:36:43 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.2.1_p111220.ebuild,v 1.1 2011/12/20 08:39:39 jlec Exp $
EAPI="3"