From 55f1746c5c695b64369ad69c38eb5bcfa2d6423f Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Fri, 11 Jul 2025 22:05:55 +0900 Subject: [PATCH 01/18] Update io.github.pemsley.coot.yaml - Replaced `--filesystem=home` with `--filesystem=host` - Added `--filesystem=xdg-cache` and `--filesystem=xdg-data` --- io.github.pemsley.coot.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/io.github.pemsley.coot.yaml b/io.github.pemsley.coot.yaml index 35d1646..2dcde3c 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -7,7 +7,9 @@ finish-args: - --socket=x11 - --share=ipc - --device=dri - - --filesystem=home + - --filesystem=host + - --filesystem=xdg-cache + - --filesystem=xdg-data - --share=network - --env=GDK_CORE_DEVICE_EVENTS=1 - --env=COOT_PREFIX=/app From fd1e2ee176dc409538972974154e2a3143e57164 Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Sun, 3 Aug 2025 13:21:12 +0900 Subject: [PATCH 02/18] gemmi: Bump to v0.7.3 --- 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 2dcde3c..4488658 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -51,14 +51,14 @@ modules: - name: gemmi buildsystem: cmake-ninja config-opts: - - -DUSE_PYTHON=1 + - -DUSE_PYTHON=ON - -DPYTHON_INSTALL_DIR=/app/lib/python3.12/site-packages build-options: cxxflags: "-fPIC -O2" sources: - type: git url: https://github.com/project-gemmi/gemmi.git - tag: v0.7.1 + tag: v0.7.3 - name: fftw2 buildsystem: autotools From 930eef74c58c066d7fafa6bf92e348972327547b Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Sun, 3 Aug 2025 13:21:51 +0900 Subject: [PATCH 03/18] coot: Bump to Release-1.1.18 --- 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 4488658..8a5ab8e 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -356,5 +356,5 @@ modules: sources: - type: git url: https://github.com/pemsley/coot.git - commit: a1e8ef5b22fcd6348807923943bd984494e594bf + tag: Release-1.1.18 From 66162883f97bc1df1f47dad420b4b5f016f93c4a Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Sun, 3 Aug 2025 13:23:32 +0900 Subject: [PATCH 04/18] Revert filesystem permissions --- io.github.pemsley.coot.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/io.github.pemsley.coot.yaml b/io.github.pemsley.coot.yaml index 8a5ab8e..9e1d989 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -7,9 +7,7 @@ finish-args: - --socket=x11 - --share=ipc - --device=dri - - --filesystem=host - - --filesystem=xdg-cache - - --filesystem=xdg-data + - --filesystem=home - --share=network - --env=GDK_CORE_DEVICE_EVENTS=1 - --env=COOT_PREFIX=/app From 5d0f39fdb4e17bbce99657de9accee071314bde7 Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Sun, 3 Aug 2025 13:29:27 +0900 Subject: [PATCH 05/18] Bump to Release-1.1.18 (#8) (#9) --- 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 b5665af..9e1d989 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -49,14 +49,14 @@ modules: - name: gemmi buildsystem: cmake-ninja config-opts: - - -DUSE_PYTHON=1 + - -DUSE_PYTHON=ON - -DPYTHON_INSTALL_DIR=/app/lib/python3.12/site-packages build-options: cxxflags: "-fPIC -O2" sources: - type: git url: https://github.com/project-gemmi/gemmi.git - tag: v0.7.1 + tag: v0.7.3 - name: fftw2 buildsystem: autotools @@ -354,5 +354,5 @@ modules: sources: - type: git url: https://github.com/pemsley/coot.git - commit: a374e0364bbe7b9eb06b5c8302db38d24ae02007 + tag: Release-1.1.18 From 2fe5a79f164c695b0d43e32ab813b17943209f68 Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Sun, 3 Aug 2025 14:41:45 +0900 Subject: [PATCH 06/18] Bump to Release-1.1.18 (#8) (#96) --- 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 b5665af..9e1d989 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -49,14 +49,14 @@ modules: - name: gemmi buildsystem: cmake-ninja config-opts: - - -DUSE_PYTHON=1 + - -DUSE_PYTHON=ON - -DPYTHON_INSTALL_DIR=/app/lib/python3.12/site-packages build-options: cxxflags: "-fPIC -O2" sources: - type: git url: https://github.com/project-gemmi/gemmi.git - tag: v0.7.1 + tag: v0.7.3 - name: fftw2 buildsystem: autotools @@ -354,5 +354,5 @@ modules: sources: - type: git url: https://github.com/pemsley/coot.git - commit: a374e0364bbe7b9eb06b5c8302db38d24ae02007 + tag: Release-1.1.18 From 6f01bd994f2cfbdd97f27871de344fe4a6d18e2f Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Sun, 3 Aug 2025 14:42:14 +0900 Subject: [PATCH 07/18] Bump to Release-1.1.18 (#94) --- 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 35d1646..9e1d989 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -49,14 +49,14 @@ modules: - name: gemmi buildsystem: cmake-ninja config-opts: - - -DUSE_PYTHON=1 + - -DUSE_PYTHON=ON - -DPYTHON_INSTALL_DIR=/app/lib/python3.12/site-packages build-options: cxxflags: "-fPIC -O2" sources: - type: git url: https://github.com/project-gemmi/gemmi.git - tag: v0.7.1 + tag: v0.7.3 - name: fftw2 buildsystem: autotools @@ -354,5 +354,5 @@ modules: sources: - type: git url: https://github.com/pemsley/coot.git - commit: a1e8ef5b22fcd6348807923943bd984494e594bf + tag: Release-1.1.18 From 70ca175ac7b9690adca1733048d22bf21c075a67 Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Wed, 6 Aug 2025 23:12:02 +0900 Subject: [PATCH 08/18] Bump to `6629ed9` (#10) --- 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 9e1d989..aca8f11 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -354,5 +354,5 @@ modules: sources: - type: git url: https://github.com/pemsley/coot.git - tag: Release-1.1.18 + commit: 6629ed951735a500eda5df8744cb20179a5a7b30 From b6a7210f9113cbcab4b20d0ca092c64da7834492 Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Thu, 7 Aug 2025 00:44:05 +0900 Subject: [PATCH 09/18] Bump to `6629ed9` (#97) --- 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 9e1d989..aca8f11 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -354,5 +354,5 @@ modules: sources: - type: git url: https://github.com/pemsley/coot.git - tag: Release-1.1.18 + commit: 6629ed951735a500eda5df8744cb20179a5a7b30 From 65160102bdd122b3235950729e8c1cbfaae6c6ae Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Mon, 25 Aug 2025 15:37:46 +0900 Subject: [PATCH 10/18] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e5637a7..0f6725f 100644 --- a/README.md +++ b/README.md @@ -28,7 +28,7 @@ flatpak run io.github.pemsley.coot **This isn’t meant to be the nightly build, but for the release that has some level of testing and is expected to mostly work and be usable to non-developer end-users.** ```shell -flatpak remote-add --if-not-exists flathub-beta https://flathub.org/beta-repo/flathub-beta.flatpakrepo +flatpak remote-add --user --if-not-exists flathub-beta https://flathub.org/beta-repo/flathub-beta.flatpakrepo flatpak install flathub-beta io.github.pemsley.coot flatpak run io.github.pemsley.coot//beta ``` From 934b8d1c690f8807116d50ad209d78599cc64235 Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Mon, 25 Aug 2025 15:38:08 +0900 Subject: [PATCH 11/18] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 0f6725f..4052d10 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,7 @@ There are two types of build for different purposes. This is the latest stable version. It is suitable for the most people for daily use. ```shell -flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo +flatpak remote-add --user --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo flatpak install flathub io.github.pemsley.coot flatpak run io.github.pemsley.coot ``` From 79310b9621b74fa0503526e9ba6427880a9cb99b Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Mon, 25 Aug 2025 07:12:31 +0000 Subject: [PATCH 12/18] Rename module 'clipper4coot' to 'clipper' --- io.github.pemsley.coot.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/io.github.pemsley.coot.yaml b/io.github.pemsley.coot.yaml index 9e1d989..769d53c 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -101,7 +101,7 @@ modules: url: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/libccp4-8.0.0.tar.gz sha256: cb813ae86612a0866329deab7cee96eac573d81be5b240341d40f9ad5322ff2d - - name: clipper4coot + - name: clipper buildsystem: autotools config-opts: - --enable-mmdb @@ -355,4 +355,3 @@ modules: - type: git url: https://github.com/pemsley/coot.git tag: Release-1.1.18 - From 2b636a99a6c196b8ea43f6dceacd0d9fe1051177 Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Mon, 25 Aug 2025 07:17:04 +0000 Subject: [PATCH 13/18] Remove redundant directory creation and add new command for monomers data --- io.github.pemsley.coot.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/io.github.pemsley.coot.yaml b/io.github.pemsley.coot.yaml index 769d53c..ebb93ac 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -345,7 +345,6 @@ modules: GLM_CFLAGS: "-I/app/include" GLM_LIBS: "-L/app/lib -lglm" post-install: - - mkdir -p ${FLATPAK_DEST}/share/coot/ - cp -r python/ ${FLATPAK_DEST}/share/coot/ - install -Dm644 pixmaps/icons/coot.svg ${FLATPAK_DEST}/share/icons/hicolor/scalable/apps/${FLATPAK_ID}.svg - install -Dm644 coot.desktop ${FLATPAK_DEST}/share/applications/${FLATPAK_ID}.desktop @@ -355,3 +354,6 @@ modules: - type: git url: https://github.com/pemsley/coot.git tag: Release-1.1.18 + - type: shell + commands: + - mkdir -p ${FLATPAK_DEST}/share/coot/lib/data/monomers From c8f3b4063a270fe865b01058e3e5eef2dfa9ed68 Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Mon, 25 Aug 2025 10:08:03 +0000 Subject: [PATCH 14/18] Replace directory creation with sed command to update Makefile.am for monomers data --- 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 ebb93ac..c9f7d45 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -356,4 +356,4 @@ modules: tag: Release-1.1.18 - type: shell commands: - - mkdir -p ${FLATPAK_DEST}/share/coot/lib/data/monomers + - sed -i '\|src ui$| s|$| monomers \\|' Makefile.am From fea27590bb7ee8a2c811c9e8d1791da643ef4594 Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Mon, 25 Aug 2025 10:38:20 +0000 Subject: [PATCH 15/18] Update sed command to correctly append monomers data in Makefile.am --- io.github.pemsley.coot.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/io.github.pemsley.coot.yaml b/io.github.pemsley.coot.yaml index c9f7d45..7b39d54 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -356,4 +356,6 @@ modules: tag: Release-1.1.18 - type: shell commands: - - sed -i '\|src ui$| s|$| monomers \\|' Makefile.am + # Workaround to add monomers data to Makefile.am + # Refer to https://github.com/pemsley/coot/issues/161#issuecomment-3219446069 + - sed -i '/python-tests cootilus fonts pyrogen data \\$/ s/$/ monomers \\/' Makefile.am From e4b976926ec158a80b37bf48c9b840ec6121a9b8 Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Mon, 25 Aug 2025 11:16:19 +0000 Subject: [PATCH 16/18] Update Makefile.am to include 'monomers' directory; refactor patch command --- Makefile.am.patch | 36 ++++++++++++++++++++++++++++++++++++ io.github.pemsley.coot.yaml | 9 ++++----- 2 files changed, 40 insertions(+), 5 deletions(-) create mode 100644 Makefile.am.patch diff --git a/Makefile.am.patch b/Makefile.am.patch new file mode 100644 index 0000000..3811247 --- /dev/null +++ b/Makefile.am.patch @@ -0,0 +1,36 @@ +diff --git a/Makefile.am b/Makefile.am +index 94227b4b7..7e1c363f0 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -1,18 +1,18 @@ + # Makefile.am +-# ++# + # Copyright 2001, 2002, 2003, 2004, 2005, 2006, 2007 The University of York + # Author: Paul Emsley +-# ++# + # This program is free software; you can redistribute it and/or modify + # it under the terms of the GNU General Public License as published by + # the Free Software Foundation; either version 3 of the License, or (at + # your option) any later version. +-# ++# + # This program is distributed in the hope that it will be useful, but + # WITHOUT ANY WARRANTY; without even the implied warranty of + # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + # General Public License for more details. +-# ++# + # You should have received a copy of the GNU General Public License + # along with this program; if not, write to the Free Software + # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA +@@ -45,7 +45,7 @@ else + SUBDIRS = auxil scheme python macros compat utils protein_db mini-mol geometry \ + lidia-core coot-utils angles ccp4mg-utils db-main analysis cootaneer ideal ligand coords \ + density-contour skeleton high-res build MoleculesToTriangles pli greg-tests \ +- python-tests cootilus fonts pyrogen data \ ++ python-tests cootilus fonts pyrogen data monomers \ + man rama-data doc glTF pixmaps textures sounds reference-structures api layla validation-graphs src ui + endif + endif diff --git a/io.github.pemsley.coot.yaml b/io.github.pemsley.coot.yaml index 7b39d54..30521a7 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -354,8 +354,7 @@ modules: - type: git url: https://github.com/pemsley/coot.git tag: Release-1.1.18 - - type: shell - commands: - # Workaround to add monomers data to Makefile.am - # Refer to https://github.com/pemsley/coot/issues/161#issuecomment-3219446069 - - sed -i '/python-tests cootilus fonts pyrogen data \\$/ s/$/ monomers \\/' Makefile.am + + # Refer to https://github.com/pemsley/coot/issues/161#issuecomment-3219446069 + - type: patch + path: Makefile.am.patch From fbcdab64054491e6993b2d4d5e6c24443163850b Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Mon, 25 Aug 2025 11:19:19 +0000 Subject: [PATCH 17/18] Refactor patch file paths in the manifest --- io.github.pemsley.coot.yaml | 8 ++++---- Makefile.am.patch => patches/Makefile.am.patch | 0 .../Makefile.template.patch | 0 .../clipper-configure-2.patch | 0 gd.h.patch => patches/gd.h.patch | 0 5 files changed, 4 insertions(+), 4 deletions(-) rename Makefile.am.patch => patches/Makefile.am.patch (100%) rename Makefile.template.patch => patches/Makefile.template.patch (100%) rename clipper-configure-2.patch => patches/clipper-configure-2.patch (100%) rename gd.h.patch => patches/gd.h.patch (100%) diff --git a/io.github.pemsley.coot.yaml b/io.github.pemsley.coot.yaml index 30521a7..8e52efd 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -118,7 +118,7 @@ modules: url: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/clipper-2.1.20180802.tar.gz sha256: 7c7774f224b59458e0faa104d209da906c129523fa737e81eb3b99ec772b81e0 - type: patch - path: clipper-configure-2.patch + path: patches/clipper-configure-2.patch - type: shell commands: - sed -i 's/libccp4c/ccp4c/g' configure @@ -133,7 +133,7 @@ modules: url: https://github.com/libgd/libgd/releases/download/gd-2.3.3/libgd-2.3.3.tar.xz sha256: 3fe822ece20796060af63b7c60acb151e5844204d289da0ce08f8fdf131e5a61 - type: patch - path: gd.h.patch + path: patches/gd.h.patch - name: raster3d buildsystem: simple @@ -148,7 +148,7 @@ modules: url: http://www.bmsc.washington.edu/raster3d/Raster3D_3.0-7.tar.gz sha256: f566b499fee341db3a95229672c6afdbdb69da7faabdbe34f6e0d332d766160c - type: patch - path: Makefile.template.patch + path: patches/Makefile.template.patch - name: ssm buildsystem: autotools @@ -357,4 +357,4 @@ modules: # Refer to https://github.com/pemsley/coot/issues/161#issuecomment-3219446069 - type: patch - path: Makefile.am.patch + path: patches/Makefile.am.patch diff --git a/Makefile.am.patch b/patches/Makefile.am.patch similarity index 100% rename from Makefile.am.patch rename to patches/Makefile.am.patch diff --git a/Makefile.template.patch b/patches/Makefile.template.patch similarity index 100% rename from Makefile.template.patch rename to patches/Makefile.template.patch diff --git a/clipper-configure-2.patch b/patches/clipper-configure-2.patch similarity index 100% rename from clipper-configure-2.patch rename to patches/clipper-configure-2.patch diff --git a/gd.h.patch b/patches/gd.h.patch similarity index 100% rename from gd.h.patch rename to patches/gd.h.patch From 67b03e0e3f6ac8ae5e251ffe1a7cce6c64a62d3e Mon Sep 17 00:00:00 2001 From: "UENO, M." Date: Thu, 9 Oct 2025 11:39:05 +0900 Subject: [PATCH 18/18] Bump to Release-1.1.19 (#12) --- io.github.pemsley.coot.yaml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/io.github.pemsley.coot.yaml b/io.github.pemsley.coot.yaml index b0426d7..5164b28 100644 --- a/io.github.pemsley.coot.yaml +++ b/io.github.pemsley.coot.yaml @@ -353,8 +353,4 @@ modules: sources: - type: git url: https://github.com/pemsley/coot.git - commit: 6629ed951735a500eda5df8744cb20179a5a7b30 - - # Refer to https://github.com/pemsley/coot/issues/161#issuecomment-3219446069 - - type: patch - path: patches/Makefile.am.patch + tag: Release-1.1.19