From 705c0f0e81455f6d8c2f73a11b22690ef35e8342 Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Fri, 6 Jun 2025 18:33:48 +0900 Subject: [PATCH 01/10] Bump to `4f510d4` --- io.github.pemsley.coot.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/io.github.pemsley.coot.yaml b/io.github.pemsley.coot.yaml index 8496f27..8762263 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -340,5 +340,5 @@ modules: sources: - type: git url: https://github.com/pemsley/coot.git - tag: Release-1.1.16 + commit: 4f510d4268047175eee71692404011f0df20f056 From 3450e11d3bc18e07acecc1168d48a4d8e686dbdd Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Fri, 6 Jun 2025 16:09:51 +0000 Subject: [PATCH 02/10] Revert boost module version from 1.88.0 to 1.87.0 --- io.github.pemsley.coot.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/io.github.pemsley.coot.yaml b/io.github.pemsley.coot.yaml index 8762263..d217adc 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -35,7 +35,7 @@ modules: - type: git url: https://github.com/project-gemmi/gemmi.git tag: v0.7.1 - + - name: fftw2 buildsystem: autotools config-opts: @@ -146,7 +146,7 @@ modules: sources: - type: git url: https://github.com/boostorg/boost.git - tag: boost-1.88.0 + tag: boost-1.87.0 - name: libdwarf buildsystem: autotools From b8f337179618031f12d44e1ad5e9c296209ee22d Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Fri, 6 Jun 2025 16:17:55 +0000 Subject: [PATCH 03/10] Bump coot module to commit `21edc3a` --- io.github.pemsley.coot.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/io.github.pemsley.coot.yaml b/io.github.pemsley.coot.yaml index d217adc..a91aaa7 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -340,5 +340,5 @@ modules: sources: - type: git url: https://github.com/pemsley/coot.git - commit: 4f510d4268047175eee71692404011f0df20f056 + commit: 21edc3a8c08602006a3d57f486444588f9326833 From 66ca2e946b51b6dc2d3407671d95ce4d61ba4d41 Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Sun, 22 Jun 2025 22:42:23 +0900 Subject: [PATCH 04/10] Bump to commit `a1e8ef5` --- io.github.pemsley.coot.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/io.github.pemsley.coot.yaml b/io.github.pemsley.coot.yaml index edac62f..c0c2d9a 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -353,4 +353,5 @@ modules: sources: - type: git url: https://github.com/pemsley/coot.git - tag: Release-1.1.17-v2 + commit: a1e8ef5b22fcd6348807923943bd984494e594bf + From 868a85e36e10b8589b82c9833236432c16828b53 Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Sun, 22 Jun 2025 14:49:40 +0000 Subject: [PATCH 05/10] Update meson-python version constraints and dependencies in requirements --- deps/pypi-dependencies.json | 14 +++++++------- deps/requirements.txt | 4 +--- 2 files changed, 8 insertions(+), 10 deletions(-) diff --git a/deps/pypi-dependencies.json b/deps/pypi-dependencies.json index e09be28..5593069 100644 --- a/deps/pypi-dependencies.json +++ b/deps/pypi-dependencies.json @@ -21,18 +21,18 @@ "name": "python3-meson-python", "buildsystem": "simple", "build-commands": [ - "pip3 install --verbose --exists-action=i --no-index --find-links=\"file://${PWD}\" --prefix=${FLATPAK_DEST} \"meson-python\" --no-build-isolation" + "pip3 install --verbose --exists-action=i --no-index --find-links=\"file://${PWD}\" --prefix=${FLATPAK_DEST} \"meson-python<0.16.0,>=0.15.0\" --no-build-isolation" ], "sources": [ { "type": "file", - "url": "https://files.pythonhosted.org/packages/7d/ec/40c0ddd29ef4daa6689a2b9c5ced47d5b58fa54ae149b19e9a97f4979c8c/meson_python-0.17.1-py3-none-any.whl", - "sha256": "30a75c52578ef14aff8392677b09c39346e0a24d2b2c6204b8ed30583c11269c" + "url": "https://files.pythonhosted.org/packages/1f/60/b10b11ab470a690d5777310d6cfd1c9bdbbb0a1313a78c34a1e82e0b9d27/meson_python-0.15.0-py3-none-any.whl", + "sha256": "3ae38253ff02b2e947a05e362a2eaf5a9a09d133c5666b4123399ee5fbf2e591" }, { "type": "file", - "url": "https://files.pythonhosted.org/packages/88/ef/eb23f262cca3c0c4eb7ab1933c3b1f03d021f2c48f54763065b6f0e321be/packaging-24.2-py3-none-any.whl", - "sha256": "09abb1bccd265c01f4a3aa3f7a7db064b36514d2cba19a2f694fe6150451a759" + "url": "https://files.pythonhosted.org/packages/20/12/38679034af332785aac8774540895e234f4d07f7545804097de4b666afd8/packaging-25.0-py3-none-any.whl", + "sha256": "29572ef2b1f17581046b3a2227d5c611fb25ec70ca1ba8554b24b0e69331a484" }, { "type": "file", @@ -50,8 +50,8 @@ "sources": [ { "type": "file", - "url": "https://files.pythonhosted.org/packages/8e/9e/dadc3831f40e22c1b3925f07894646ada7906ef5b48db5c5eb2b03ca9faa/nanobind-2.5.0-py3-none-any.whl", - "sha256": "e1e5c816e5d10f0b252d82ba7f769f0f6679f5e043cf406aec3d9e184bf2a60d" + "url": "https://files.pythonhosted.org/packages/96/14/989883082b395146120d34ca7e484a2b24cb73b0e428576a3a4249bd4082/nanobind-2.7.0-py3-none-any.whl", + "sha256": "73b12d0e751d140d6c1bf4b215e18818a8debfdb374f08dc3776ad208d808e74" } ] }, diff --git a/deps/requirements.txt b/deps/requirements.txt index 48b7bea..58d363e 100644 --- a/deps/requirements.txt +++ b/deps/requirements.txt @@ -1,6 +1,4 @@ -mako -markdown markupsafe -meson-python +meson-python>=0.15.0,<0.16.0 nanobind numpy==1.26.4 From c41fc26d305a15307954ee213bd4fa0447ab4e38 Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Sun, 22 Jun 2025 14:50:42 +0000 Subject: [PATCH 06/10] Change the order of installation of openblas module to first --- io.github.pemsley.coot.yaml | 39 +++++++++++++++++++------------------ 1 file changed, 20 insertions(+), 19 deletions(-) diff --git a/io.github.pemsley.coot.yaml b/io.github.pemsley.coot.yaml index edac62f..3d73c1f 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -24,6 +24,26 @@ cleanup: - "*.a" modules: + - name: openblas + buildsystem: cmake-ninja + builddir: true + config-opts: + - -DUSE_OPENMP=ON + - -DNUM_THREADS=64 + - -DNO_SVE=ON + - -DBUILD_SHARED_LIBS=ON + - -DDYNAMIC_ARCH=ON + build-options: + cflags: "-fPIC -O3" + post-install: + - ln -s /app/lib/libopenblas.so /app/lib/libblas.so + - ln -s /app/lib/libopenblas.so /app/lib/liblapack.so + sources: + - type: archive + url: https://github.com/OpenMathLib/OpenBLAS/archive/refs/tags/v0.3.28.tar.gz + sha256: f1003466ad074e9b0c8d421a204121100b0751c96fc6fcf3d1456bd12f8a00a1 + + # markupsafe, meson-python, nanobind, numpy - deps/pypi-dependencies.json - name: gemmi @@ -184,25 +204,6 @@ modules: url: https://github.com/g-truc/glm/archive/refs/tags/1.0.1.tar.gz sha256: 9f3174561fd26904b23f0db5e560971cbf9b3cbda0b280f04d5c379d03bf234c - - name: openblas - buildsystem: cmake-ninja - builddir: true - config-opts: - - -DUSE_OPENMP=ON - - -DNUM_THREADS=64 - - -DNO_SVE=ON - - -DBUILD_SHARED_LIBS=ON - - -DDYNAMIC_ARCH=ON - build-options: - cflags: "-fPIC -O3" - post-install: - - ln -s /app/lib/libopenblas.so /app/lib/libblas.so - - ln -s /app/lib/libopenblas.so /app/lib/liblapack.so - sources: - - type: archive - url: https://github.com/OpenMathLib/OpenBLAS/archive/refs/tags/v0.3.28.tar.gz - sha256: f1003466ad074e9b0c8d421a204121100b0751c96fc6fcf3d1456bd12f8a00a1 - - name: bdw-gc buildsystem: autotools config-opts: From 80c33f10f3aee66b5ae41774c9d233f2ca71cc64 Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Mon, 23 Jun 2025 03:17:40 +0000 Subject: [PATCH 07/10] Add Cython dependency to requirements and include Cython source in pypi-dependencies --- deps/pypi-dependencies.json | 7 ++++++- deps/requirements.txt | 1 + 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/deps/pypi-dependencies.json b/deps/pypi-dependencies.json index 5593069..61ad54a 100644 --- a/deps/pypi-dependencies.json +++ b/deps/pypi-dependencies.json @@ -62,6 +62,11 @@ "pip3 install --verbose --exists-action=i --no-index --find-links=\"file://${PWD}\" --prefix=${FLATPAK_DEST} \"numpy==1.26.4\" --no-build-isolation" ], "sources": [ + { + "type": "file", + "url": "https://files.pythonhosted.org/packages/5a/25/886e197c97a4b8e254173002cdc141441e878ff29aaa7d9ba560cd6e4866/cython-3.0.12.tar.gz", + "sha256": "b988bb297ce76c671e28c97d017b95411010f7c77fa6623dd0bb47eed1aee1bc" + }, { "type": "file", "url": "https://files.pythonhosted.org/packages/65/6e/09db70a523a96d25e115e71cc56a6f9031e7b8cd166c1ac8438307c14058/numpy-1.26.4.tar.gz", @@ -70,4 +75,4 @@ ] } ] -} \ No newline at end of file +} diff --git a/deps/requirements.txt b/deps/requirements.txt index 58d363e..25d3001 100644 --- a/deps/requirements.txt +++ b/deps/requirements.txt @@ -1,3 +1,4 @@ +Cython>=0.29.34,<3.1 markupsafe meson-python>=0.15.0,<0.16.0 nanobind From baa3fe7f9b511f40e4858b0c9b38648df3b2e5c6 Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Mon, 23 Jun 2025 03:57:19 +0000 Subject: [PATCH 08/10] Modify pypi-dependencies.sh for numpy handling --- deps/pypi-dependencies.json | 4 ++-- deps/pypi-dependencies.sh | 3 ++- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/deps/pypi-dependencies.json b/deps/pypi-dependencies.json index 61ad54a..9081445 100644 --- a/deps/pypi-dependencies.json +++ b/deps/pypi-dependencies.json @@ -21,7 +21,7 @@ "name": "python3-meson-python", "buildsystem": "simple", "build-commands": [ - "pip3 install --verbose --exists-action=i --no-index --find-links=\"file://${PWD}\" --prefix=${FLATPAK_DEST} \"meson-python<0.16.0,>=0.15.0\" --no-build-isolation" + "pip3 install --verbose --exists-action=i --no-index --find-links=\"file://${PWD}\" --prefix=${FLATPAK_DEST} \"meson-python>=0.15.0,<0.16.0\" --no-build-isolation" ], "sources": [ { @@ -59,7 +59,7 @@ "name": "python3-numpy", "buildsystem": "simple", "build-commands": [ - "pip3 install --verbose --exists-action=i --no-index --find-links=\"file://${PWD}\" --prefix=${FLATPAK_DEST} \"numpy==1.26.4\" --no-build-isolation" + "pip3 install --verbose --exists-action=i --no-index --find-links=\"file://${PWD}\" --prefix=${FLATPAK_DEST} \"numpy==1.26.4\" --ignore-installed --no-build-isolation" ], "sources": [ { diff --git a/deps/pypi-dependencies.sh b/deps/pypi-dependencies.sh index 2a7a990..2adfcdd 100755 --- a/deps/pypi-dependencies.sh +++ b/deps/pypi-dependencies.sh @@ -1,3 +1,4 @@ #!/usr/bin/env bash -./flatpak-builder-tools/pip/flatpak-pip-generator --runtime='org.gnome.Sdk//48' --requirements-file='requirements.txt' --output pypi-dependencies +# Cython version corresponding to the specified numpy version must be manually added to pypi-dependencies.json afterwards +./flatpak-builder-tools/pip/flatpak-pip-generator --runtime='org.gnome.Sdk//48' --requirements-file='requirements.txt' --output=pypi-dependencies --ignore-installed=numpy From 6c2b81f8508cb0bf25929bfe425d53e1bcf85fe3 Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Mon, 23 Jun 2025 03:57:37 +0000 Subject: [PATCH 09/10] Change OpenBLAS source from archive to git for improved version control --- io.github.pemsley.coot.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/io.github.pemsley.coot.yaml b/io.github.pemsley.coot.yaml index 3d73c1f..58a95ee 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -39,9 +39,9 @@ modules: - ln -s /app/lib/libopenblas.so /app/lib/libblas.so - ln -s /app/lib/libopenblas.so /app/lib/liblapack.so sources: - - type: archive - url: https://github.com/OpenMathLib/OpenBLAS/archive/refs/tags/v0.3.28.tar.gz - sha256: f1003466ad074e9b0c8d421a204121100b0751c96fc6fcf3d1456bd12f8a00a1 + - type: git + url: https://github.com/OpenMathLib/OpenBLAS.git + tag: v0.3.28 # markupsafe, meson-python, nanobind, numpy - deps/pypi-dependencies.json From ee23dff47ca2a89b44decc0475c9e60b0ff7c145 Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Mon, 23 Jun 2025 04:23:27 +0000 Subject: [PATCH 10/10] Add Cython in pypi-dependencies.json and update requirements.txt --- deps/pypi-dependencies.json | 15 ++++++++++++--- deps/requirements.txt | 1 - 2 files changed, 12 insertions(+), 4 deletions(-) diff --git a/deps/pypi-dependencies.json b/deps/pypi-dependencies.json index 9081445..8673944 100644 --- a/deps/pypi-dependencies.json +++ b/deps/pypi-dependencies.json @@ -56,17 +56,26 @@ ] }, { - "name": "python3-numpy", + "name": "python3-Cython", "buildsystem": "simple", "build-commands": [ - "pip3 install --verbose --exists-action=i --no-index --find-links=\"file://${PWD}\" --prefix=${FLATPAK_DEST} \"numpy==1.26.4\" --ignore-installed --no-build-isolation" + "pip3 install --verbose --exists-action=i --no-index --find-links=\"file://${PWD}\" --prefix=${FLATPAK_DEST} \"cython==3.0.12\" --ignore-installed --no-build-isolation" ], "sources": [ { "type": "file", "url": "https://files.pythonhosted.org/packages/5a/25/886e197c97a4b8e254173002cdc141441e878ff29aaa7d9ba560cd6e4866/cython-3.0.12.tar.gz", "sha256": "b988bb297ce76c671e28c97d017b95411010f7c77fa6623dd0bb47eed1aee1bc" - }, + } + ] + }, + { + "name": "python3-numpy", + "buildsystem": "simple", + "build-commands": [ + "pip3 install --verbose --exists-action=i --no-index --find-links=\"file://${PWD}\" --prefix=${FLATPAK_DEST} \"numpy==1.26.4\" --ignore-installed --no-build-isolation" + ], + "sources": [ { "type": "file", "url": "https://files.pythonhosted.org/packages/65/6e/09db70a523a96d25e115e71cc56a6f9031e7b8cd166c1ac8438307c14058/numpy-1.26.4.tar.gz", diff --git a/deps/requirements.txt b/deps/requirements.txt index 25d3001..58d363e 100644 --- a/deps/requirements.txt +++ b/deps/requirements.txt @@ -1,4 +1,3 @@ -Cython>=0.29.34,<3.1 markupsafe meson-python>=0.15.0,<0.16.0 nanobind