gentoo auto-resync : 29:09:2024 - 01:25:46

9 files changed, 492 insertions, 0 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index e2d3b7d6c932..a46ec2c846c6 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index c2aeb2fb9df4..1352ddf62ff9 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,5 +1,12 @@
 AUX pymol-2.5.0-format-security.patch 562 BLAKE2B 566f653ca3abd4498f9ee5d7255e1b06d8df320bd25a569620b1ee33da0cfb6a969fd3e0a65fbce7116cd6567d9a544c57f4d6d399bec00b9effa8273a52153c SHA512 4e93a0449470abdbd2d943ef0a5fac7f302485ca42c6d9ccdf1ab9a879029d5185c3f1a3a2e237fd8b3b3bf0a306bce07db3226257360127c97546480c233c4f
+AUX pymol-3.0.0-SceneGetDrawFlag-indexing.patch 821 BLAKE2B c854aa49441b308ab7f12265442961ddeb3633b71234bd554d45c3950c3ddcf457ac98e0aa1d226ec7ee3abbd2d0207cce97e40144cb81992f241c3a964b1bcc SHA512 326e04f988ff585a062a342b9553ab6b074102c0599b210a5dfa769cb8841e1619e74b670a2d673a80b81c5a9218e052829e0cc574049a1363741e762cac59e7
+AUX pymol-3.0.0-distutils-py3.12.patch 2620 BLAKE2B 802ef75cf22b408ff8e280c561f4954f7f4d816887107f8db36b85988c345948e7d2cfe97b099cb79794d61d3594666e12f90a64c1f0af2206458ade776a1a2b SHA512 3911207f1a03b19675105cd707d644e76258aa9ab58be3891833873d41b460f6161ac83d495a6bc58bf281831376d17186083d447269d755d2e69ee78e6fc5c2
+AUX pymol-3.0.0-eof-maeffplugin.patch 1071 BLAKE2B b28941bd3fddb534fe150b3d98ef6a17058b25b59717a15ca9a807812f05d98f3f7b2cedee9230eab0465c493bbf375325259260bb1cd0d03beafbb4a8f306d0 SHA512 b39846fa9b3b90d5952f22fdde323039bd09a5c43abdd7975bc72880854f22ae39a0d3d30a6640e98c6d7e8734306e00af3fdae555a4292e48ad7b46a83753f8
+AUX pymol-3.0.0-lto-molfile-plugin.patch 5585 BLAKE2B d9cedbb270184d562373fc9e8a2e1a75b08c5d1a956c28eac55662b424996a6770ea46d45b0645a7b96ab465af0f6aafac3120ed13a29f12daea5ab7c947da5d SHA512 babe47d4cbea390031d1880cf442c780f442d41bdeb181509df307550aa8d9c829af51a676665e8d55ed4cd6ab3f2cde363a087606cb064238bbc74be7e2fe51
+AUX pymol-3.0.0-numpy2.patch 1203 BLAKE2B bd06e70fea5a9a4940ecea226f2bd8d1f4753826ee246d6d418cd473c0ee738b9373c8f6e2f5e56e3708ab2934486286d43c33441e1e97f819c6ac0af731d060 SHA512 2c9445f013383fb534dca4306fa5f8ab8f55b33ed4bc53617e7765cb708a4ebc5380f8578ea1236f61e9e77a6d5a8e21588f7f081f6d6408195b9fa5b67c60b2
+AUX pymol-3.0.0-py3.12-progress.patch 985 BLAKE2B 77103dc94b2e9e304f65e429f5abb1cd2158d95a0b8b53e90d7e915b213a934ea8a598240355437b00cf95e0203c382d003034fa30a37dc00758351d13163e38 SHA512 ff7b75402a92d491145e1487fa018182a2a5a91f1736c63d07a194e6710d425f1bba59a7b4f0f49321e27db8c05e26feda7df12f42a66b1e1cdbf1e52f869a5b
 DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
 DIST pymol-3.0.0.tar.gz 29510174 BLAKE2B b67818e408045e386e44a203f29cd94a0ce34ec706776d29f78f1720bdc5c79d88f3b3e178882295b5a636d97fe70ff49eb1b021a9a6b96f0f4216bc392219d1 SHA512 eab05a46220339a05d8d4facdce6bfa08c6fc8a858a7b228236ef6c4054207059ef0f53a26bedebe4084a74b510015937fb4477f99612b21412cd75bf0c376a2
+EBUILD pymol-3.0.0-r1.ebuild 3372 BLAKE2B 378b1587c25a4592b6e2e503e7280f38d44696a899d5931c6f3e5a2ef11ed5f28d2bd9ba2e8024e6ed223d6bf504a2b76f7b730926eac7bbdbfbb29f986b3287 SHA512 597918ca799ceb6b2a29704ddc96e2b67464d66dd27ce6d32b00294854d34a4abbeb340848f2d3101464b6f263fb4dd07314c54d14fb87be57b07a27ae06522a
 EBUILD pymol-3.0.0.ebuild 2958 BLAKE2B 2eac68b0cf15c3369e243b7456e00b1c1119f0d8399bea7321794981f41911bd56bc10713c9102475a054e6a52353cef63c0f9416974bb1db5d91ddd9f6d2dfa SHA512 ca7a597cd909d5a04e77c0afb7e2c07413b13dd42d5788db97defabee23370695299e17193b431eb6190c87a0e06d8e741d2067de973652d1749b244cfeb0254
 MISC metadata.xml 495 BLAKE2B 32d321e92c7e7c226747660c314f5cff9aabf9ee41c8a864064432ac9554879db7bf60640993dadae6e00a9b7d1367cb8ab228b63b8797ca84e5618eeeb192cc SHA512 36ef956d111c76182c70c81a830885f540fb2710f696b2711837d4bf1055a8792226f38b827f389a3a3861f259bae1394d6da50c2b33a0ddb4e6940262e1b25d
diff --git a/sci-chemistry/pymol/files/pymol-3.0.0-SceneGetDrawFlag-indexing.patch b/sci-chemistry/pymol/files/pymol-3.0.0-SceneGetDrawFlag-indexing.patch
new file mode 100644
index 000000000000..c23bf79d6166
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-3.0.0-SceneGetDrawFlag-indexing.patch
@@ -0,0 +1,22 @@
+From 50be59fb4bd6706c7939a659f4477041e2f0619e Mon Sep 17 00:00:00 2001
+From: Jarrett Johnson <36459667+JarrettSJohnson@users.noreply.github.com>
+Date: Sat, 6 Apr 2024 22:49:41 -0400
+Subject: [PATCH] PYMOL-4849: Fix SceneGetDrawFlag slot indexing
+
+---
+ layer1/Scene.cpp | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/layer1/Scene.cpp b/layer1/Scene.cpp
+index e4888db6d..ed211bdd6 100644
+--- a/layer1/Scene.cpp
++++ b/layer1/Scene.cpp
+@@ -4448,7 +4448,7 @@ int SceneGetDrawFlag(GridInfo * grid, int *slot_vla, int slot)
+       {
+         if(((slot < 0) && grid->slot) ||
+            ((slot == 0) && (grid->slot == 0)) ||
+-           (slot_vla && (slot_vla[slot] == grid->slot))) {
++           (slot_vla && (slot >= 0 && slot_vla[slot] == grid->slot))) {
+           draw_flag = true;
+         }
+       }
diff --git a/sci-chemistry/pymol/files/pymol-3.0.0-distutils-py3.12.patch b/sci-chemistry/pymol/files/pymol-3.0.0-distutils-py3.12.patch
new file mode 100644
index 000000000000..3ab0384bd5f6
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-3.0.0-distutils-py3.12.patch
@@ -0,0 +1,70 @@
+From 3d3c8963798d426e70675c3c40df146e12869b0a Mon Sep 17 00:00:00 2001
+From: Branch Vincent <branchevincent@gmail.com>
+Date: Fri, 10 May 2024 22:12:58 -0700
+Subject: [PATCH] replace distutils for python 3.12 (#362)
+
+Co-authored-by: Jarrett Johnson <jarrett.johnson@schrodinger.com>
+---
+ create_shadertext.py                  | 3 +--
+ modules/pymol/plugins/installation.py | 7 +++----
+ testing/tests/system/pymolwin.py      | 1 -
+ 3 files changed, 4 insertions(+), 7 deletions(-)
+
+diff --git a/create_shadertext.py b/create_shadertext.py
+index 7bae72180..f6857087e 100644
+--- a/create_shadertext.py
++++ b/create_shadertext.py
+@@ -7,7 +7,6 @@
+ from collections import defaultdict
+ from os.path import dirname
+ from subprocess import Popen, PIPE
+-from distutils import dir_util
+ 
+ def create_all(generated_dir, pymoldir="."):
+     '''
+@@ -30,7 +29,7 @@ def __init__(self, filename):
+             self.out = cStringIO.StringIO()
+             self.filename = filename
+         else:
+-            dir_util.mkpath(os.path.dirname(filename))
++            os.makedirs(os.path.dirname(filename), exist_ok=True)
+             self.out = open(filename, "w")
+             self.filename = None
+     def close(self):
+diff --git a/modules/pymol/plugins/installation.py b/modules/pymol/plugins/installation.py
+index 3a980545b..2fb8f6f03 100644
+--- a/modules/pymol/plugins/installation.py
++++ b/modules/pymol/plugins/installation.py
+@@ -45,8 +45,6 @@ def cmp_version(v1, v2):
+     '''
+     Compares two version strings. An empty version string is always considered
+     smaller than a non-empty version string.
+-
+-    Uses distutils.version.StrictVersion to evaluate non-empty version strings.
+     '''
+     if v1 == v2:
+         return 0
+@@ -55,8 +53,9 @@ def cmp_version(v1, v2):
+     if v2 == '':
+         return 1
+     try:
+-        from distutils.version import StrictVersion as Version
+-        return cmp(Version(v1), Version(v2))
++        v1_parts = list(map(int, v1.split('.')))
++        v2_parts = list(map(int, v2.split('.')))
++        return (v1_parts > v2_parts) - (v1_parts < v2_parts)
+     except:
+         print(' Warning: Version parsing failed for', v1, 'and/or', v2)
+         return 0
+diff --git a/testing/tests/system/pymolwin.py b/testing/tests/system/pymolwin.py
+index 429fd28aa..e7885bd38 100644
+--- a/testing/tests/system/pymolwin.py
++++ b/testing/tests/system/pymolwin.py
+@@ -7,7 +7,6 @@
+ import subprocess

+ import sys

+ import unittest

+-from distutils.spawn import find_executable

+ from pymol import cmd, CmdException, testing, stored

+ 

+ @unittest.skipIf(not sys.platform.startswith('win'), 'windows only')

diff --git a/sci-chemistry/pymol/files/pymol-3.0.0-eof-maeffplugin.patch b/sci-chemistry/pymol/files/pymol-3.0.0-eof-maeffplugin.patch
new file mode 100644
index 000000000000..8eb8fbde318b
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-3.0.0-eof-maeffplugin.patch
@@ -0,0 +1,22 @@
+From f005dde377e3e50b6e3f405939435c5061fa8b63 Mon Sep 17 00:00:00 2001
+From: Jarrett Johnson <36459667+JarrettSJohnson@users.noreply.github.com>
+Date: Mon, 22 Apr 2024 11:12:21 -0400
+Subject: [PATCH] PYMOL-4869: Only compare eof token in maeffplugin parser
+
+---
+ contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp b/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp
+index efaede65b..0547ff91b 100644
+--- a/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp
++++ b/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp
+@@ -248,7 +248,7 @@ const char * Tokenizer::token(bool ignore_single) {
+   char c = peek();
+   bool good = false;
+   ssize_t diff;
+-  while(state != DONE && c >= 0) {
++  while(state != DONE && c != std::char_traits<char>::eof()) {
+     // make sure we have space in m_token for 2 more characters
+     if ((diff = ptr-m_token) >= max_token_size-1) {
+       m_token = (char *)realloc( m_token, 2*max_token_size );
diff --git a/sci-chemistry/pymol/files/pymol-3.0.0-lto-molfile-plugin.patch b/sci-chemistry/pymol/files/pymol-3.0.0-lto-molfile-plugin.patch
new file mode 100644
index 000000000000..445fc6bc3a10
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-3.0.0-lto-molfile-plugin.patch
@@ -0,0 +1,187 @@
+From 9d3061ca58d8b69d7dad74a68fc13fe81af0ff8e Mon Sep 17 00:00:00 2001
+From: Jarrett Johnson <jarrett.johnson@schrodinger.com>
+Date: Thu, 5 Sep 2024 11:20:02 -0400
+Subject: [PATCH] Symbol renaming in molfile_plugin and internal linkage
+
+Fixes #395
+---
+ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h    | 10 +++++-----
+ .../uiuc/plugins/molfile_plugin/src/parm7plugin.cpp    |  8 +++++---
+ contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp |  2 ++
+ layer0/Isosurf.cpp                                     |  6 ++++--
+ layer0/Tetsurf.cpp                                     |  6 ++++--
+ ov/src/OVOneToAny.cpp                                  |  2 ++
+ ov/src/OVOneToOne.cpp                                  |  2 ++
+ 7 files changed, 24 insertions(+), 12 deletions(-)
+
+diff --git a/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h b/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h
+index 21d967d79..6bd6ddb08 100644
+--- a/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h
++++ b/contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h
+@@ -59,7 +59,7 @@
+ #endif
+ 
+ 
+-typedef struct parm {
++typedef struct parm7 {
+   char title[85];
+   char version[85];
+   int   IfBox, Nmxrs, IfCap,
+@@ -70,7 +70,7 @@ typedef struct parm {
+         Ipatm, Natcap,Ifpert,Nbper,Ngper,Ndper,Mbper,Mgper,Mdper,
+         Numextra;
+   _REAL Box[3], Cutcap, Xcap, Ycap, Zcap;
+-} parmstruct;
++} parm7struct;
+ 
+ static int read_parm7_flag(FILE *file, const char *flag, const char *format) {
+   char buf[1024];
+@@ -359,10 +359,10 @@ static void close_parm7_file(FILE *fileptr, int popn) {
+ 
+ static const char *parm7 = "%8d%8d%8d%8d%8d%8d%8d%8d%8d%8d\n";
+ 
+-static parmstruct *read_parm7_header(FILE *file) {
++static parm7struct *read_parm7_header(FILE *file) {
+   char sdum[512]; 
+-  parmstruct *prm;
+-  prm = new parmstruct;
++  parm7struct *prm;
++  prm = new parm7struct;
+ 
+   /* READ VERSION */
+   fgets(sdum, 512, file);
+diff --git a/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp b/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp
+index faf2717c6..2d46553b4 100644
+--- a/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp
++++ b/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp
+@@ -24,13 +24,15 @@
+ #include "molfile_plugin.h"
+ #include "ReadPARM7.h"
+ 
++namespace {
+ typedef struct {
+-  parmstruct *prm;
++  parm7struct *prm;
+   int popn;
+   FILE *fd;
+   int nbonds;
+   int *from, *to;
+ } parmdata;
++}
+ 
+ static void *open_parm7_read(const char *filename, const char *,int *natoms) {
+   FILE *fd;
+@@ -39,7 +41,7 @@ static void *open_parm7_read(const char *filename, const char *,int *natoms) {
+     fprintf(stderr, "parm7plugin) Cannot open parm file '%s'\n", filename);
+     return NULL;
+   }
+-  parmstruct *prm = read_parm7_header(fd);
++  parm7struct *prm = read_parm7_header(fd);
+   if (!prm) {
+     close_parm7_file(fd, popn);
+     return NULL; 
+@@ -58,7 +60,7 @@ static void *open_parm7_read(const char *filename, const char *,int *natoms) {
+ 
+ static int read_parm7_structure(void *mydata, int *optflags, molfile_atom_t *atoms) {
+   parmdata *p = (parmdata *)mydata;
+-  const parmstruct *prm = p->prm;
++  const parm7struct *prm = p->prm;
+   FILE *file = p->fd;
+   char buf[85];
+   char field[85];
+diff --git a/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp b/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp
+index acabcb1b5..4996383e1 100644
+--- a/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp
++++ b/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp
+@@ -24,12 +24,14 @@
+ #include "ReadPARM.h"
+ #include "molfile_plugin.h"
+ 
++namespace {
+ typedef struct {
+   ReadPARM *rp;
+   FILE *parm;
+   int natoms;
+   int *from, *to;
+ } parmdata;
++}
+ 
+ static void *open_parm_read(const char *filename, const char *, 
+     int *natoms) {
+diff --git a/layer0/Isosurf.cpp b/layer0/Isosurf.cpp
+index 77cf42eeb..b2dfaedd7 100644
+--- a/layer0/Isosurf.cpp
++++ b/layer0/Isosurf.cpp
+@@ -44,11 +44,13 @@ Z* -------------------------------------------------------------------
+ 
+ #define I4(field,P1,P2,P3,P4) ((field)->get<int>(P1,P2,P3,P4))
+ 
+-typedef struct PointType {
++namespace {
++struct PointType {
+   float Point[3];
+   int NLink;
+   struct PointType* Link[4];
+-} PointType;
++};
++}
+ 
+ #define EdgePtPtr(field,P2,P3,P4,P5) ((field)->ptr(P2,P3,P4,P5))
+ 
+diff --git a/layer0/Tetsurf.cpp b/layer0/Tetsurf.cpp
+index 0d78b535e..cb2f5b37b 100644
+--- a/layer0/Tetsurf.cpp
++++ b/layer0/Tetsurf.cpp
+@@ -38,12 +38,14 @@ Z* -------------------------------------------------------------------
+ 
+ #define I3(field,P1,P2,P3) ((field)->get<int>(P1,P2,P3))
+ 
+-typedef struct {
++namespace {
++struct PointType {
+   float Point[3];
+   float Normal[3];
+   int NormalFlag;
+   int Link;
+-} PointType;
++};
++}
+ 
+ typedef struct {
+   PointType *p[3];
+diff --git a/ov/src/OVOneToAny.cpp b/ov/src/OVOneToAny.cpp
+index 1a675a51b..5dbbc498c 100644
+--- a/ov/src/OVOneToAny.cpp
++++ b/ov/src/OVOneToAny.cpp
+@@ -8,11 +8,13 @@
+ 
+ /* FYI: "up" stands for UniquePair -- a precursor to OneToAny */
+ 
++namespace {
+ typedef struct {
+   int active;
+   ov_word forward_value, reverse_value;
+   ov_size forward_next;
+ } up_element;
++}
+ 
+ struct _OVOneToAny {
+   OVHeap *heap;
+diff --git a/ov/src/OVOneToOne.cpp b/ov/src/OVOneToOne.cpp
+index 6dfa8f457..4e9baf9c6 100644
+--- a/ov/src/OVOneToOne.cpp
++++ b/ov/src/OVOneToOne.cpp
+@@ -8,11 +8,13 @@
+ 
+ /* FYI: "up" stands for UniquePair -- a precursor to OneToOne */
+ 
++namespace {
+ typedef struct {
+   int active;
+   ov_word forward_value, reverse_value;
+   ov_size forward_next, reverse_next;
+ } up_element;
++}
+ 
+ struct _OVOneToOne {
+   OVHeap *heap;
diff --git a/sci-chemistry/pymol/files/pymol-3.0.0-numpy2.patch b/sci-chemistry/pymol/files/pymol-3.0.0-numpy2.patch
new file mode 100644
index 000000000000..7cf2884ee201
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-3.0.0-numpy2.patch
@@ -0,0 +1,35 @@
+From 758cec338057b23007ffd14c960634ff0ee24af1 Mon Sep 17 00:00:00 2001
+From: Jarrett Johnson <jarrett.johnson@schrodinger.com>
+Date: Tue, 27 Aug 2024 20:06:57 -0400
+Subject: [PATCH] Make numpy2 compatible
+
+---
+ layer2/ObjectMap.cpp    | 1 +
+ modules/chempy/brick.py | 2 +-
+ 2 files changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/layer2/ObjectMap.cpp b/layer2/ObjectMap.cpp
+index ada826f8a..62e3457a4 100644
+--- a/layer2/ObjectMap.cpp
++++ b/layer2/ObjectMap.cpp
+@@ -5596,6 +5596,7 @@ static int ObjectMapNumPyArrayToMapState(PyMOLGlobals * G, ObjectMapState * ms,
+   void * ptr;
+ 
+ #ifdef _PYMOL_NUMPY
++  import_array1(0);
+   PyArrayObject * pao = (PyArrayObject *) ary;
+   const int itemsize = PyArray_ITEMSIZE(pao);
+ #endif
+diff --git a/modules/chempy/brick.py b/modules/chempy/brick.py
+index fc514eb3a..e4c0f1bbb 100644
+--- a/modules/chempy/brick.py
++++ b/modules/chempy/brick.py
+@@ -31,7 +31,7 @@ def from_numpy(cls, data, grid, origin=(0.0, 0.0, 0.0)):
+         @param range: 3f sequence
+         @param origin: 3f sequence
+         '''
+-        data = numpy.asfarray(data)
++        data = numpy.asarray(data, dtype=numpy.float64)
+         assert len(data.shape) == 3
+ 
+         self = cls()
diff --git a/sci-chemistry/pymol/files/pymol-3.0.0-py3.12-progress.patch b/sci-chemistry/pymol/files/pymol-3.0.0-py3.12-progress.patch
new file mode 100644
index 000000000000..b09f36048b20
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-3.0.0-py3.12-progress.patch
@@ -0,0 +1,26 @@
+From 11325a6014565700be9673236c9b7b6c856ea6d9 Mon Sep 17 00:00:00 2001
+From: Jarrett Johnson <jarrett.johnson@schrodinger.com>
+Date: Wed, 28 Aug 2024 22:07:15 -0400
+Subject: [PATCH] Python 3.12 TypeError: convert progress to int for progress
+ bar
+
+---
+ modules/pmg_qt/pymol_qt_gui.py | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/modules/pmg_qt/pymol_qt_gui.py b/modules/pmg_qt/pymol_qt_gui.py
+index f2d663204..6e935b0d6 100644
+--- a/modules/pmg_qt/pymol_qt_gui.py
++++ b/modules/pmg_qt/pymol_qt_gui.py
+@@ -929,9 +929,9 @@ def command_set_cursor(self, i):
+         return self.lineedit.setCursorPosition(i)
+ 
+     def update_progress(self):
+-        progress = self.cmd.get_progress()
++        progress = int(self.cmd.get_progress() * 100)
+         if progress >= 0:
+-            self.progressbar.setValue(progress * 100)
++            self.progressbar.setValue(progress)
+             self.progressbar.show()
+             self.abortbutton.show()
+         else:
diff --git a/sci-chemistry/pymol/pymol-3.0.0-r1.ebuild b/sci-chemistry/pymol/pymol-3.0.0-r1.ebuild
new file mode 100644
index 000000000000..aeb6bc85c7e1
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-3.0.0-r1.ebuild
@@ -0,0 +1,123 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..12} )
+DISTUTILS_USE_PEP517="setuptools"
+DISTUTILS_EXT=1
+
+inherit desktop flag-o-matic xdg distutils-r1
+
+DESCRIPTION="A Python-extensible molecular graphics system"
+HOMEPAGE="https://www.pymol.org/"
+SRC_URI="https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+S="${WORKDIR}"/${PN}-open-source-${PV}
+
+LICENSE="BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA" #844991
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="+netcdf web"
+
+DEPEND="
+	dev-cpp/msgpack-cxx
+	dev-libs/mmtf-cpp
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sys-libs/zlib
+	media-libs/freetype:2
+	media-libs/glew:0=
+	media-libs/glm
+	media-libs/libpng:0=
+	netcdf? ( sci-libs/netcdf:0= )
+"
+BDEPEND="test? ( >=dev-cpp/catch-2:0 )"
+RDEPEND="
+	${DEPEND}
+	media-video/mpeg-tools
+	dev-python/pyopengl[${PYTHON_USEDEP}]
+	dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
+	dev-python/pmw[${PYTHON_USEDEP}]
+	sci-chemistry/chemical-mime-data
+"
+
+distutils_enable_tests pytest
+
+# FIXME: We need to still figure out about how to make all the tests pass
+# https://bugs.gentoo.org/932127
+RESTRICT="test"
+
+PATCHES=(
+	"${FILESDIR}/${P}-distutils-py3.12.patch"
+	"${FILESDIR}/${P}-SceneGetDrawFlag-indexing.patch"
+	"${FILESDIR}/${P}-eof-maeffplugin.patch"
+	"${FILESDIR}/${P}-numpy2.patch"
+	"${FILESDIR}/${P}-py3.12-progress.patch"
+	"${FILESDIR}/${P}-lto-molfile-plugin.patch"
+)
+
+python_prepare_all() {
+	sed \
+		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
+		-e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
+		-i setup.py || die
+
+	sed \
+		-e "s:/opt/local:${EPREFIX}/usr:g" \
+		-e '/ext_comp_args/s:\[.*\]:[]:g' \
+		-i setup.py || die
+	sed \
+		-e "s:\['msgpackc'\]:\['msgpack'\]:g" \
+		-i setup.py || die
+
+	append-cxxflags -std=c++17
+
+	distutils-r1_python_prepare_all
+}
+
+python_configure_all() {
+	use !netcdf && DISTUTILS_ARGS=( --no-vmd-plugins )
+}
+
+python_install() {
+	distutils-r1_python_install \
+		--pymol-path="${EPREFIX}/usr/share/pymol"
+
+	sed \
+		-e '1i#!/usr/bin/env python' \
+		"${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die
+	python_doscript "${T}"/${PN}
+}
+
+python_test() {
+	"${EPYTHON}" -m pymol -ckqy testing/testing.py --offline --no-mmlibs --no-undo --run all || die
+}
+
+python_install_all() {
+	distutils-r1_python_install_all
+
+	# Move data to correct location
+	dodir /usr/share/pymol
+	mv "${D}/$(python_get_sitedir)"/pymol/pymol_path/* "${ED}/usr/share/pymol" || die
+
+	# These environment variables should not go in the wrapper script, or else
+	# it will be impossible to use the PyMOL libraries from Python.
+	cat >> "${T}"/20pymol <<- EOF || die
+		PYMOL_PATH="${EPREFIX}/usr/share/pymol"
+		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
+		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
+	EOF
+
+	doenvd "${T}"/20pymol
+
+	newicon "${S}"/data/pymol/icons/icon2.svg ${PN}.svg
+	make_desktop_entry "${PN} %u"  PyMol ${PN} \
+		"Graphics;Education;Science;Chemistry;" \
+		"MimeType=chemical/x-pdb;chemical/pdby;chemical/x-mdl-sdfile;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;chemical/x-macromodel-input;chemical/x-vmd;"
+
+	if ! use web; then
+		rm -rf "${D}/$(python_get_sitedir)/web" || die
+	fi
+
+	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
+}