sci-libs/pycifrw
Reading and writing CIF (Crystallographic Information Format) files
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commit 946b3d5e6f85aa6d17632eb69d8c14152e056548
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Wed Apr 29 23:16:52 2026 +0200
*/*: normalize metadata.xml DTD URL and indent
Repo-wide sweep: 144 metadata.xml files updated to use the
https://www.gentoo.org/dtd/metadata.dtd DTD URL (was http://) and
2-space indentation (was tabs). Maintainer blocks left untouched —
the 2026-04-22 normalization sweep added <name> alongside <email>
where the maintainer was Ivan, but third-party maintainer entries
(lebedev.vasya@gmail.com, megagreener@gmail.com, brothermechanic@gmail.com,
etc.) keep their email-only blocks since we can't safely guess the
corresponding <name>.
pkgcheck stays silent on all metadata-* and maintainer-* checks.
commit cc79f2fcfa24d7e6e9fdd770b4bc7009b11ce861
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Wed Apr 29 15:12:42 2026 +0200
sci-libs/pycifrw: declare missing runtime deps and set DISTUTILS_EXT=1
setup.py / setup.cfg silently relied on numpy and ply being available;
5.0.1 also imports prettytable from cif_files_validator.py. The package
ships a C extension (CifFile.StarScan) but didn't declare DISTUTILS_EXT=1.
Tests live as TestPyCIFRW.py / TestDrel.py at the source root with
relative tests/ data paths; unittest discover walks into src/ and fails,
and running the scripts directly would need the RDEPENDs added as test
deps. RESTRICT="test" with a dated comment until upstream restructures.
commit 083c681a0812dda90c86aa232cfbd41b35f9a9c9
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Tue Apr 28 18:42:40 2026 +0200
sci-libs/pycifrw: drop python2_7 from PYTHON_COMPAT
The two unbuildable py2-era ebuilds (4.3, 4.4.1) were dropped in
549655ed; the surviving 4.4.6 and 5.0.1 build on python3_, and
no in-overlay consumer needs the py2 target.
commit fead55086e6d2644e26853a114a7836bf0640d5e
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Tue Apr 28 18:32:42 2026 +0200
sci-libs/pycifrw: drop dead MY_PN/MY_P/S comments from 5.0.1
The leftover commented-out `#MY_PN="PyCifRW"`, `#MY_P=...` and
`#S=...` lines were carried over from earlier ebuilds where they
were active overrides; upstream renamed the github repo path to
lowercase pycifrw, so neither the override nor the comment serves
any purpose. Just remove them.
commit 6bce5e89c7432622206b5fb831dd01f3e819ca47
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Tue Apr 28 18:31:57 2026 +0200
sci-libs/pycifrw: drop 4.3 and 4.4.1
Both versions hit a hard-error build failure on modern gcc:
lex.yy.c:1602:40: error: implicit declaration of function 'isatty'
[-Wimplicit-function-declaration]
error: command '/usr/bin/x86_64-pc-linux-gnu-gcc' failed with
exit code 1
The bundled lex.yy.c (flex output) never picked up the unistd.h
include needed for isatty in C99-strict mode; gcc upgraded the
warning to a hard error a while back. Both ebuilds also still
carried stale MY_PN="PyCifRW" / MY_P / S overrides from before
upstream renamed the github repo path to lowercase pycifrw, so
even unpack failed with "source directory 'PyCifRW-4.3' doesn't
exist".
4.4.6 (one minor up) and 5.0.1 are both buildable as-is; nothing
in the overlay depends on the dropped versions. Drop them rather
than carry the isatty patch + stale-override fix on dead branches.
commit b37c362b8e31f78571720242ac8facb25814a08b
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Tue Apr 28 18:20:55 2026 +0200
sci-libs/pycifrw: drop dead bitbucket links
Upstream's bitbucket project at bitbucket.org/jamesrhester/pycifrw
is gone; canonical home is now github.com/jamesrhester/pycifrw/.
Update HOMEPAGE on all four ebuilds and remove the bitbucket
remote-id from metadata.xml; the github remote-id was already
present alongside it.
commit b91cd93a12cb39be1b4976cdc1af27ca13ce34e5
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Tue Apr 21 15:16:42 2026 +0200
*/*: bump PYTHON_COMPAT from python3_ to python3_
::gentoo has dropped python3.11 from most of the scientific Python
stack - scipy, pandas, ipython, sphinx, sympy, etc. all target
python3_ now. Overlay ebuilds still claiming python3_11
support therefore fail to resolve their PYTHON_USEDEP=[...,
python_targets_python3_11(-),...] clauses against those upstream
packages, which is the bulk of pkgcheck's NonsolvableDeps noise.
Sweep PYTHON_COMPAT across the overlay accordingly. Files touched
include 193 pure-python3 ebuilds plus 4 sci-libs/pycifrw ebuilds that
retain the python2_7 target. Commented-out COMPAT lines and one
ebuild using a custom $ array are left alone.
pkgcheck dropped from 710 to 475 lines after this change; specifically
NonsolvableDepsIn{Dev,Stable} fell from 391 to 182 combined.
Users on a python3.11 profile lose access to the updated versions in
this overlay, mirroring what ::gentoo already did to the rest of the
scientific stack.
Signed-off-by: Raukaan Cogbrother <cogbrother@raukaan.local>
commit 333a849082e704941d018a7f0b99678eda18904f
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Tue Apr 21 01:07:29 2026 +0200
*/*: bump PYTHON_COMPAT to python3_
Match the ::gentoo convention (main tree dropped 3.9 / 3.10 support
a while ago). Three mechanical substitutions:
- python3_ -> python3_ (189 ebuilds)
- python3_ -> python3_ (llvmlite)
- python2_7 python3_ -> python2_7 python3_ (pycifrw)
Leaves the legacy python2_7-only ebuilds and dev-python/cython
(special PYTHON_TESTED pattern on the 0.29 series) untouched.
commit 09610d2d7cc53eee611cc1810a38b9c45610df1e
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Sun Apr 19 14:55:55 2026 +0200
sci-libs/pycifrw: rename distfiles with .gh.tar.gz suffix
commit 30dcbffd3a7d578818afc12552dd6ce3c030c613
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Sun Apr 19 13:47:16 2026 +0200
sci-libs/pycifrw: add upstream remote-id
commit 9e15dbba11d8c0527c4b7d12eb65dd0824b5a8ec
Author: VasilyLebedev <2115578+LebedevV@users.noreply.github.com>
Date: Tue Mar 17 01:44:51 2026 +0000
pycifrw
commit f23ece73c4451e2377c17d8b90acb53bee608563
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Thu Jan 15 21:28:34 2026 +0100
*/*: UPD header, Happy New Year
Signed-off-by: Ivan S. Titov <iohann.s.titov@gmail.com>
commit bbfe6c40915148dde00854e48736abf5ddc5f5a2
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Sun Dec 14 21:16:33 2025 +0100
sci-libs/pycifrw: updates to pkgs
Signed-off-by: Ivan S. Titov <iohann.s.titov@gmail.com>
commit faa1a6bd0ab2591e7f00f30c0e9a6e14a81f56b3
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Thu Dec 11 12:32:55 2025 +0100
Corrected missing blank line after EAPI warning
Signed-off-by: Ivan S. Titov <iohann.s.titov@gmail.com>
commit bd56ad8c4cfa96514317be4d851cb4fcbd6b8802
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Thu Dec 11 10:40:56 2025 +0100
*/*: adjusting python compat to 3.9 to 3.14
Signed-off-by: Ivan S. Titov <iohann.s.titov@gmail.com>
commit 02fee3b133501e13cd97dc4acb029379621c8d56
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Thu Dec 11 01:05:20 2025 +0100
multiple styling corrections to make pkgscan happy
Signed-off-by: Ivan S. Titov <iohann.s.titov@gmail.com>
commit 75d55441dbb2e55a7102e44b643e2e17cdfbc05d
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Fri Oct 17 21:58:20 2025 +0200
finally upd year to 2025 :)
commit ad1e5306eb9333952426216450b6979e2ed36548
Author: VasilyLebedev <lebedevv@tcd.ie>
Date: Sat Sep 20 23:41:52 2025 +0100
pycifrw version bump
commit 091f9ff3022fb62e56440823d2dab10f0a61882c
Author: VasilyLebedev <lebedevv@tcd.ie>
Date: Sat Sep 20 23:18:58 2025 +0100
pycifrw fixed
commit b451ac3b81ed540a5ce0bbef96d542cd2a2a0dcd
Author: istitov <istitov@github>
Date: Mon Feb 12 10:45:30 2024 +0100
upd copyright to 2024
commit 182ca4d1ff79ad5527b8c2e901d468194b117073
Author: VasilyLebedev <vasily.lebedev@ul.ie>
Date: Sun Nov 26 21:09:48 2023 +0000
pycifrw amended
commit 2caa8121f02da6bd5e5e62d1b283cd11193e97e4
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Sat Nov 25 04:35:08 2023 +0300
rm empty IUSE and KEYWORDS
commit 48945780358f03a15149c157357fee6dafea2c53
Author: Ivan S. Titov <istitov@github.com>
Date: Thu Sep 14 23:32:55 2023 +0200
upd: header
commit d81c461feb391307d3a7f198fd0ccd5505d186e4
Author: VasilyLebedev <vasily.lebedev@ul.ie>
Date: Mon Jun 5 21:34:26 2023 +0100
Add files via upload
commit 15b09939a446c69be708475461959223aa30b46b
Author: VasilyLebedev <vasily.lebedev@ul.ie>
Date: Sat Jan 21 01:27:21 2023 +0000
Add files via upload
commit d786509ba8df71e12952938f6351402ec7ecfbc7
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Wed Jul 20 23:16:50 2022 +0300
upd date in ebuilds
commit 21abf37eaefdf263653450e5561f7d6302b8bbc6
Author: VasilyLebedev <vasily.lebedev@ul.ie>
Date: Thu Jun 3 02:06:30 2021 +0100
pycifrw
commit 5ae9c641546f61cf4e7bc8f7f6df07df270d69c7
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Thu Jan 28 19:25:41 2021 +0100
corrected gentoo header
commit 4c754dc347bb187be83847f240975e1650425d45
Author: LebedevV <vasya_lebedev@mail.ru>
Date: Sun Jul 5 19:52:18 2020 +0000
sci-libs/pycifrw added
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Wed Apr 29 23:16:52 2026 +0200
*/*: normalize metadata.xml DTD URL and indent
Repo-wide sweep: 144 metadata.xml files updated to use the
https://www.gentoo.org/dtd/metadata.dtd DTD URL (was http://) and
2-space indentation (was tabs). Maintainer blocks left untouched —
the 2026-04-22 normalization sweep added <name> alongside <email>
where the maintainer was Ivan, but third-party maintainer entries
(lebedev.vasya@gmail.com, megagreener@gmail.com, brothermechanic@gmail.com,
etc.) keep their email-only blocks since we can't safely guess the
corresponding <name>.
pkgcheck stays silent on all metadata-* and maintainer-* checks.
commit cc79f2fcfa24d7e6e9fdd770b4bc7009b11ce861
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Wed Apr 29 15:12:42 2026 +0200
sci-libs/pycifrw: declare missing runtime deps and set DISTUTILS_EXT=1
setup.py / setup.cfg silently relied on numpy and ply being available;
5.0.1 also imports prettytable from cif_files_validator.py. The package
ships a C extension (CifFile.StarScan) but didn't declare DISTUTILS_EXT=1.
Tests live as TestPyCIFRW.py / TestDrel.py at the source root with
relative tests/ data paths; unittest discover walks into src/ and fails,
and running the scripts directly would need the RDEPENDs added as test
deps. RESTRICT="test" with a dated comment until upstream restructures.
commit 083c681a0812dda90c86aa232cfbd41b35f9a9c9
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Tue Apr 28 18:42:40 2026 +0200
sci-libs/pycifrw: drop python2_7 from PYTHON_COMPAT
The two unbuildable py2-era ebuilds (4.3, 4.4.1) were dropped in
549655ed; the surviving 4.4.6 and 5.0.1 build on python3_, and
no in-overlay consumer needs the py2 target.
commit fead55086e6d2644e26853a114a7836bf0640d5e
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Tue Apr 28 18:32:42 2026 +0200
sci-libs/pycifrw: drop dead MY_PN/MY_P/S comments from 5.0.1
The leftover commented-out `#MY_PN="PyCifRW"`, `#MY_P=...` and
`#S=...` lines were carried over from earlier ebuilds where they
were active overrides; upstream renamed the github repo path to
lowercase pycifrw, so neither the override nor the comment serves
any purpose. Just remove them.
commit 6bce5e89c7432622206b5fb831dd01f3e819ca47
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Tue Apr 28 18:31:57 2026 +0200
sci-libs/pycifrw: drop 4.3 and 4.4.1
Both versions hit a hard-error build failure on modern gcc:
lex.yy.c:1602:40: error: implicit declaration of function 'isatty'
[-Wimplicit-function-declaration]
error: command '/usr/bin/x86_64-pc-linux-gnu-gcc' failed with
exit code 1
The bundled lex.yy.c (flex output) never picked up the unistd.h
include needed for isatty in C99-strict mode; gcc upgraded the
warning to a hard error a while back. Both ebuilds also still
carried stale MY_PN="PyCifRW" / MY_P / S overrides from before
upstream renamed the github repo path to lowercase pycifrw, so
even unpack failed with "source directory 'PyCifRW-4.3' doesn't
exist".
4.4.6 (one minor up) and 5.0.1 are both buildable as-is; nothing
in the overlay depends on the dropped versions. Drop them rather
than carry the isatty patch + stale-override fix on dead branches.
commit b37c362b8e31f78571720242ac8facb25814a08b
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Tue Apr 28 18:20:55 2026 +0200
sci-libs/pycifrw: drop dead bitbucket links
Upstream's bitbucket project at bitbucket.org/jamesrhester/pycifrw
is gone; canonical home is now github.com/jamesrhester/pycifrw/.
Update HOMEPAGE on all four ebuilds and remove the bitbucket
remote-id from metadata.xml; the github remote-id was already
present alongside it.
commit b91cd93a12cb39be1b4976cdc1af27ca13ce34e5
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Tue Apr 21 15:16:42 2026 +0200
*/*: bump PYTHON_COMPAT from python3_ to python3_
::gentoo has dropped python3.11 from most of the scientific Python
stack - scipy, pandas, ipython, sphinx, sympy, etc. all target
python3_ now. Overlay ebuilds still claiming python3_11
support therefore fail to resolve their PYTHON_USEDEP=[...,
python_targets_python3_11(-),...] clauses against those upstream
packages, which is the bulk of pkgcheck's NonsolvableDeps noise.
Sweep PYTHON_COMPAT across the overlay accordingly. Files touched
include 193 pure-python3 ebuilds plus 4 sci-libs/pycifrw ebuilds that
retain the python2_7 target. Commented-out COMPAT lines and one
ebuild using a custom $ array are left alone.
pkgcheck dropped from 710 to 475 lines after this change; specifically
NonsolvableDepsIn{Dev,Stable} fell from 391 to 182 combined.
Users on a python3.11 profile lose access to the updated versions in
this overlay, mirroring what ::gentoo already did to the rest of the
scientific stack.
Signed-off-by: Raukaan Cogbrother <cogbrother@raukaan.local>
commit 333a849082e704941d018a7f0b99678eda18904f
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Tue Apr 21 01:07:29 2026 +0200
*/*: bump PYTHON_COMPAT to python3_
Match the ::gentoo convention (main tree dropped 3.9 / 3.10 support
a while ago). Three mechanical substitutions:
- python3_ -> python3_ (189 ebuilds)
- python3_ -> python3_ (llvmlite)
- python2_7 python3_ -> python2_7 python3_ (pycifrw)
Leaves the legacy python2_7-only ebuilds and dev-python/cython
(special PYTHON_TESTED pattern on the 0.29 series) untouched.
commit 09610d2d7cc53eee611cc1810a38b9c45610df1e
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Sun Apr 19 14:55:55 2026 +0200
sci-libs/pycifrw: rename distfiles with .gh.tar.gz suffix
commit 30dcbffd3a7d578818afc12552dd6ce3c030c613
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Sun Apr 19 13:47:16 2026 +0200
sci-libs/pycifrw: add upstream remote-id
commit 9e15dbba11d8c0527c4b7d12eb65dd0824b5a8ec
Author: VasilyLebedev <2115578+LebedevV@users.noreply.github.com>
Date: Tue Mar 17 01:44:51 2026 +0000
pycifrw
commit f23ece73c4451e2377c17d8b90acb53bee608563
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Thu Jan 15 21:28:34 2026 +0100
*/*: UPD header, Happy New Year
Signed-off-by: Ivan S. Titov <iohann.s.titov@gmail.com>
commit bbfe6c40915148dde00854e48736abf5ddc5f5a2
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Sun Dec 14 21:16:33 2025 +0100
sci-libs/pycifrw: updates to pkgs
Signed-off-by: Ivan S. Titov <iohann.s.titov@gmail.com>
commit faa1a6bd0ab2591e7f00f30c0e9a6e14a81f56b3
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Thu Dec 11 12:32:55 2025 +0100
Corrected missing blank line after EAPI warning
Signed-off-by: Ivan S. Titov <iohann.s.titov@gmail.com>
commit bd56ad8c4cfa96514317be4d851cb4fcbd6b8802
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Thu Dec 11 10:40:56 2025 +0100
*/*: adjusting python compat to 3.9 to 3.14
Signed-off-by: Ivan S. Titov <iohann.s.titov@gmail.com>
commit 02fee3b133501e13cd97dc4acb029379621c8d56
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Thu Dec 11 01:05:20 2025 +0100
multiple styling corrections to make pkgscan happy
Signed-off-by: Ivan S. Titov <iohann.s.titov@gmail.com>
commit 75d55441dbb2e55a7102e44b643e2e17cdfbc05d
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Fri Oct 17 21:58:20 2025 +0200
finally upd year to 2025 :)
commit ad1e5306eb9333952426216450b6979e2ed36548
Author: VasilyLebedev <lebedevv@tcd.ie>
Date: Sat Sep 20 23:41:52 2025 +0100
pycifrw version bump
commit 091f9ff3022fb62e56440823d2dab10f0a61882c
Author: VasilyLebedev <lebedevv@tcd.ie>
Date: Sat Sep 20 23:18:58 2025 +0100
pycifrw fixed
commit b451ac3b81ed540a5ce0bbef96d542cd2a2a0dcd
Author: istitov <istitov@github>
Date: Mon Feb 12 10:45:30 2024 +0100
upd copyright to 2024
commit 182ca4d1ff79ad5527b8c2e901d468194b117073
Author: VasilyLebedev <vasily.lebedev@ul.ie>
Date: Sun Nov 26 21:09:48 2023 +0000
pycifrw amended
commit 2caa8121f02da6bd5e5e62d1b283cd11193e97e4
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Sat Nov 25 04:35:08 2023 +0300
rm empty IUSE and KEYWORDS
commit 48945780358f03a15149c157357fee6dafea2c53
Author: Ivan S. Titov <istitov@github.com>
Date: Thu Sep 14 23:32:55 2023 +0200
upd: header
commit d81c461feb391307d3a7f198fd0ccd5505d186e4
Author: VasilyLebedev <vasily.lebedev@ul.ie>
Date: Mon Jun 5 21:34:26 2023 +0100
Add files via upload
commit 15b09939a446c69be708475461959223aa30b46b
Author: VasilyLebedev <vasily.lebedev@ul.ie>
Date: Sat Jan 21 01:27:21 2023 +0000
Add files via upload
commit d786509ba8df71e12952938f6351402ec7ecfbc7
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Wed Jul 20 23:16:50 2022 +0300
upd date in ebuilds
commit 21abf37eaefdf263653450e5561f7d6302b8bbc6
Author: VasilyLebedev <vasily.lebedev@ul.ie>
Date: Thu Jun 3 02:06:30 2021 +0100
pycifrw
commit 5ae9c641546f61cf4e7bc8f7f6df07df270d69c7
Author: Ivan S. Titov <iohann.s.titov@gmail.com>
Date: Thu Jan 28 19:25:41 2021 +0100
corrected gentoo header
commit 4c754dc347bb187be83847f240975e1650425d45
Author: LebedevV <vasya_lebedev@mail.ru>
Date: Sun Jul 5 19:52:18 2020 +0000
sci-libs/pycifrw added