From 178d863f7b0c387f893d891cb118004f26b2e23f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tom=20David=20M=C3=BCller?= Date: Sat, 29 Jun 2024 13:10:44 +0200 Subject: [PATCH 01/43] add packaging step --- ...uild-windows-executable-app-with-pyinstaller.yaml | 12 ++++++++++++ .github/workflows/build-windows-executable-app.yaml | 12 ++++++++++++ 2 files changed, 24 insertions(+) diff --git a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml index b956775e..fd4cf18f 100644 --- a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml +++ b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml @@ -130,6 +130,18 @@ jobs: CCACHE_COMPRESSLEVEL: 12 CCACHE_MAXSIZE: 400M + - name: Package + shell: bash + run: | + ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cipackage.cmake + env: + SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS" + PACKAGE_TYPE: nsis + SEARCH_ENGINES_DIRECTORY: "${{ github.workspace }}/_thirdparty" + CI_PROVIDER: "GitHub-Actions" + PACK_ZIP: 1 + CPACK_PACKAGE_FILE_NAME: "openms-package" + - name: Test Windows shell: bash run: $LAUNCHER ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index a0de350b..c91920ec 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -134,6 +134,18 @@ jobs: CCACHE_COMPRESSLEVEL: 12 CCACHE_MAXSIZE: 400M + - name: Package + shell: bash + run: | + ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cipackage.cmake + env: + SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS" + PACKAGE_TYPE: nsis + SEARCH_ENGINES_DIRECTORY: "${{ github.workspace }}/_thirdparty" + CI_PROVIDER: "GitHub-Actions" + PACK_ZIP: 1 + CPACK_PACKAGE_FILE_NAME: "openms-package" + - name: Test Windows shell: bash run: $LAUNCHER ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake From 5263becd1bdf864cd38aba6999907f301b000de9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tom=20David=20M=C3=BCller?= Date: Sat, 29 Jun 2024 13:14:16 +0200 Subject: [PATCH 02/43] use package instead of bin share artifacts --- ...ndows-executable-app-with-pyinstaller.yaml | 42 +++++++------------ .../build-windows-executable-app.yaml | 38 +++++++---------- 2 files changed, 30 insertions(+), 50 deletions(-) diff --git a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml index fd4cf18f..357d7716 100644 --- a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml +++ b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml @@ -151,17 +151,11 @@ jobs: CI_PROVIDER: "GitHub-Actions" BUILD_NAME: "${{ env.RUN_NAME }}-Win64-class-topp-${{ github.run_number }}" - - name: Upload TOPP tools as artifact - uses: actions/upload-artifact@v3 + - name: Upload package as artifact + uses: actions/upload-artifact@v4 with: - name: OpenMS-bin - path: OpenMS/bld/bin - - - name: Upload share as artifact - uses: actions/upload-artifact@v3 - with: - name: OpenMS-share - path: OpenMS/share + name: openms-package + path: ${{ github.workspace }}/OpenMS/bld/*.zip build-executable: runs-on: windows-latest @@ -174,17 +168,18 @@ jobs: - name: Checkout uses: actions/checkout@v3 - - name: Download TOPP tools as artifact - uses: actions/download-artifact@v3 + - name: Download package as artifact + uses: actions/download-artifact@v4 with: - name: OpenMS-bin - path: openms-bin + name: openms-package + path: openms-package - - name: Download share as artifact - uses: actions/download-artifact@v3 - with: - name: OpenMS-share - path: share + - name: Extract bin and share from package + run: | + cd openms-package + unzip "*.zip" -d . + cp -r openms-package/bin ../openms-bin + cp -r openms-package/share ../share - name: Set up Python uses: actions/setup-python@v4 @@ -248,15 +243,10 @@ jobs: call myenv\Scripts\activate.bat pyinstaller run_app.spec --clean - - name: Delete OpenMS bin artifact - uses: geekyeggo/delete-artifact@v2 - with: - name: OpenMS-bin - - - name: Delete OpenMS share artifact + - name: Delete OpenMS package artifact uses: geekyeggo/delete-artifact@v2 with: - name: OpenMS-share + name: openms-package - name: Upload artifact uses: actions/upload-artifact@v3 diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index c91920ec..e1a9e3e7 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -155,17 +155,11 @@ jobs: CI_PROVIDER: "GitHub-Actions" BUILD_NAME: "${{ env.RUN_NAME }}-Win64-class-topp-${{ github.run_number }}" - - name: Upload TOPP tools as artifact + - name: Upload package as artifact uses: actions/upload-artifact@v4 with: - name: OpenMS-bin - path: OpenMS/bld/bin - - - name: Upload share as artifact - uses: actions/upload-artifact@v4 - with: - name: OpenMS-share - path: OpenMS/share + name: openms-package + path: ${{ github.workspace }}/OpenMS/bld/*.zip build-executable: runs-on: windows-latest @@ -178,17 +172,18 @@ jobs: - name: Checkout uses: actions/checkout@v4 - - name: Download TOPP tools as artifact + - name: Download package as artifact uses: actions/download-artifact@v4 with: - name: OpenMS-bin - path: openms-bin + name: openms-package + path: openms-package - - name: Download share as artifact - uses: actions/download-artifact@v4 - with: - name: OpenMS-share - path: share + - name: Extract bin and share from package + run: | + cd openms-package + unzip "*.zip" -d . + cp -r openms-package/bin ../openms-bin + cp -r openms-package/share ../share - name: Setup python embeddable version run: | @@ -229,15 +224,10 @@ jobs: cp -r share streamlit_exe/share cp app.py streamlit_exe - - name: Delete OpenMS bin artifact - uses: geekyeggo/delete-artifact@v4 - with: - name: OpenMS-bin - - - name: Delete OpenMS share artifact + - name: Delete OpenMS package artifact uses: geekyeggo/delete-artifact@v2 with: - name: OpenMS-share + name: openms-package - name: Compress streamlit_exe folder to OpenMS-App.zip run: | From ffd2ed5e0de7c0a826e21f18d8d6027fb6f551d2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tom=20David=20M=C3=BCller?= Date: Sat, 29 Jun 2024 19:34:32 +0200 Subject: [PATCH 03/43] add topp tool selection --- ...ild-windows-executable-app-with-pyinstaller.yaml | 13 +++++++++---- .github/workflows/build-windows-executable-app.yaml | 13 +++++++++---- 2 files changed, 18 insertions(+), 8 deletions(-) diff --git a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml index b956775e..00f6d1d8 100644 --- a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml +++ b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml @@ -1,14 +1,15 @@ name: Build executable for Windows with pyinstaller on: workflow_dispatch: +env: + OPENMS_VERSION: 3.0.0 + # Define needed TOPP tools here + TOPP_TOOLS: "FeatureFinderMetabo MetaboliteAdductDecharger SiriusExport" jobs: build-openms: runs-on: windows-latest - env: - OPENMS_VERSION: 3.0.0 - steps: - name: Checkout uses: actions/checkout@v3 @@ -221,9 +222,13 @@ jobs: cp -r src dist/src cp -r assets dist/assets cp -r example-data dist/example-data - cp -r openms-bin dist/bin cp -r share dist/share cp app.py dist/ + + $files = $env:TOPP_TOOLS -split ' ' + foreach ($file in $files) { + Copy-Item "openms-bin/${file}.exe" -Destination "dist/bin/${file}.exe" + } - name: Modify .spec file shell: bash diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index a0de350b..6abb3351 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -5,14 +5,15 @@ on: pull_request: branches: [ "main" ] workflow_dispatch: +env: + OPENMS_VERSION: 3.0.0 + # Define needed TOPP tools here + TOPP_TOOLS: "FeatureFinderMetabo MetaboliteAdductDecharger SiriusExport" jobs: build-openms: runs-on: windows-latest - env: - OPENMS_VERSION: 3.0.0 - steps: - name: Checkout uses: actions/checkout@v4 @@ -213,10 +214,14 @@ jobs: cp -r assets streamlit_exe cp -r example-data streamlit_exe cp -r .streamlit streamlit_exe - cp -r openms-bin streamlit_exe/bin cp -r share streamlit_exe/share cp app.py streamlit_exe + $files = $env:TOPP_TOOLS -split ' ' + foreach ($file in $files) { + Copy-Item "openms-bin/${file}.exe" -Destination "streamlit_exe/bin/${file}.exe" + } + - name: Delete OpenMS bin artifact uses: geekyeggo/delete-artifact@v4 with: From 46ce7c312c3b5753fef3272172f675d3ddb8c0e5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tom=20David=20M=C3=BCller?= Date: Sat, 29 Jun 2024 21:24:56 +0200 Subject: [PATCH 04/43] copy dlls and create folder --- .../build-windows-executable-app-with-pyinstaller.yaml | 4 ++++ .github/workflows/build-windows-executable-app.yaml | 3 +++ 2 files changed, 7 insertions(+) diff --git a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml index 00f6d1d8..e5b1d933 100644 --- a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml +++ b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml @@ -217,11 +217,15 @@ jobs: - name: Copy everything to dist directory run: | + mkdir dist + mkdir dist/bin + cp -r .streamlit dist/.streamlit cp -r pages dist/pages cp -r src dist/src cp -r assets dist/assets cp -r example-data dist/example-data + cp openms-bin/*.dll streamlit_exe/bin/ cp -r share dist/share cp app.py dist/ diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index 6abb3351..e1b768da 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -207,12 +207,15 @@ jobs: - name: Create All-in-one executable folder run: | mkdir streamlit_exe + mkdir streamlit_exe/bin + mv python-${{ env.PYTHON_VERSION }} streamlit_exe mv run_app.bat streamlit_exe cp -r src streamlit_exe cp -r pages streamlit_exe cp -r assets streamlit_exe cp -r example-data streamlit_exe + cp openms-bin/*.dll streamlit_exe/bin/ cp -r .streamlit streamlit_exe cp -r share streamlit_exe/share cp app.py streamlit_exe From 0414325a9700f7a055ba709fd2464347fc70fb27 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tom=20David=20M=C3=BCller?= Date: Tue, 2 Jul 2024 17:21:32 +0200 Subject: [PATCH 05/43] update delete artifact --- .../build-windows-executable-app-with-pyinstaller.yaml | 2 +- .github/workflows/build-windows-executable-app.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml index 357d7716..a38d7ec7 100644 --- a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml +++ b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml @@ -244,7 +244,7 @@ jobs: pyinstaller run_app.spec --clean - name: Delete OpenMS package artifact - uses: geekyeggo/delete-artifact@v2 + uses: geekyeggo/delete-artifact@v5 with: name: openms-package diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index e1a9e3e7..497e4488 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -225,7 +225,7 @@ jobs: cp app.py streamlit_exe - name: Delete OpenMS package artifact - uses: geekyeggo/delete-artifact@v2 + uses: geekyeggo/delete-artifact@v5 with: name: openms-package From 3f340bb6b8f3b78a9a9a19124f617c3f85ab36ce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tom=20David=20M=C3=BCller?= Date: Thu, 4 Jul 2024 11:55:40 +0200 Subject: [PATCH 06/43] adjust packaging flags --- .../build-windows-executable-app-with-pyinstaller.yaml | 3 +-- .github/workflows/build-windows-executable-app.yaml | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml index a38d7ec7..5459d49e 100644 --- a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml +++ b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml @@ -136,10 +136,9 @@ jobs: ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cipackage.cmake env: SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS" - PACKAGE_TYPE: nsis + PACKAGE_TYPE: zip SEARCH_ENGINES_DIRECTORY: "${{ github.workspace }}/_thirdparty" CI_PROVIDER: "GitHub-Actions" - PACK_ZIP: 1 CPACK_PACKAGE_FILE_NAME: "openms-package" - name: Test Windows diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index 497e4488..f0f47d01 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -140,10 +140,9 @@ jobs: ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cipackage.cmake env: SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS" - PACKAGE_TYPE: nsis + PACKAGE_TYPE: zip SEARCH_ENGINES_DIRECTORY: "${{ github.workspace }}/_thirdparty" CI_PROVIDER: "GitHub-Actions" - PACK_ZIP: 1 CPACK_PACKAGE_FILE_NAME: "openms-package" - name: Test Windows From f7b12e688e95f22dc52410d00c646c85e0f0eaf3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tom=20David=20M=C3=BCller?= Date: Tue, 13 Aug 2024 14:03:47 +0200 Subject: [PATCH 07/43] temporarily point to develop --- .../build-windows-executable-app-with-pyinstaller.yaml | 3 ++- .github/workflows/build-windows-executable-app.yaml | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml index e5b1d933..0e4c19da 100644 --- a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml +++ b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml @@ -15,7 +15,8 @@ jobs: uses: actions/checkout@v3 with: repository: OpenMS/OpenMS - ref: release/${{ env.OPENMS_VERSION }} + # ref: release/${{ env.OPENMS_VERSION }} + ref: develop path: 'OpenMS' - name: Install Qt diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index e1b768da..222a111e 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -19,7 +19,8 @@ jobs: uses: actions/checkout@v4 with: repository: OpenMS/OpenMS - ref: release/${{ env.OPENMS_VERSION }} + # ref: release/${{ env.OPENMS_VERSION }} + ref: develop path: 'OpenMS' - name: Install Qt From 7e068117304ba4658bb27b9abdfba048eb3fbe2d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tom=20David=20M=C3=BCller?= <57191390+t0mdavid-m@users.noreply.github.com> Date: Wed, 25 Sep 2024 10:08:49 +0200 Subject: [PATCH 08/43] update openms version --- .../build-windows-executable-app-with-pyinstaller.yaml | 2 +- .github/workflows/build-windows-executable-app.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml index 70d8e30c..7fc29869 100644 --- a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml +++ b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml @@ -2,7 +2,7 @@ name: Build executable for Windows with pyinstaller on: workflow_dispatch: env: - OPENMS_VERSION: 3.0.0 + OPENMS_VERSION: 3.2.0 # Define needed TOPP tools here TOPP_TOOLS: "FeatureFinderMetabo MetaboliteAdductDecharger SiriusExport" diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index be6fa140..5e096dbf 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -6,7 +6,7 @@ on: branches: [ "main" ] workflow_dispatch: env: - OPENMS_VERSION: 3.0.0 + OPENMS_VERSION: 3.2.0 # Define needed TOPP tools here TOPP_TOOLS: "FeatureFinderMetabo MetaboliteAdductDecharger SiriusExport" From 1096eb853eede2b5df884081f5fd904625f4bec0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tom=20David=20M=C3=BCller?= <57191390+t0mdavid-m@users.noreply.github.com> Date: Wed, 25 Sep 2024 10:27:36 +0200 Subject: [PATCH 09/43] fix ref --- .../build-windows-executable-app-with-pyinstaller.yaml | 3 +-- .github/workflows/build-windows-executable-app.yaml | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml index 02b685af..c7967163 100644 --- a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml +++ b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml @@ -15,8 +15,7 @@ jobs: uses: actions/checkout@v3 with: repository: OpenMS/OpenMS - # ref: release/${{ env.OPENMS_VERSION }} - ref: develop + ref: release/${{ env.OPENMS_VERSION }} path: 'OpenMS' - name: Install Qt diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index 43d7c452..d16c5028 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -19,8 +19,7 @@ jobs: uses: actions/checkout@v4 with: repository: OpenMS/OpenMS - # ref: release/${{ env.OPENMS_VERSION }} - ref: develop + ref: release/${{ env.OPENMS_VERSION }} path: 'OpenMS' - name: Install Qt From ba646bef6ec805be1b93e644f941677d91280ca8 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 25 Sep 2024 10:48:08 +0200 Subject: [PATCH 10/43] fix build path --- .github/workflows/build-windows-executable-app.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index d16c5028..cd8bd5f8 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -110,7 +110,7 @@ jobs: shell: bash run: | mkdir $GITHUB_WORKSPACE/OpenMS/bld/ - ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cibuild.cmake + ctest --output-on-failure -V -S OpenMS/tools/ci/cibuild.cmake env: #OS_PREFIX_PATH: "${{ env.Qt5_DIR }}/lib/cmake;${{ env.Qt5_DIR }}" CONTRIB_BUILD_DIRECTORY: "${{ github.workspace }}/OpenMS/contrib" From e72f64e830080ff5747ed633719567786d25954b Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 25 Sep 2024 11:52:36 +0200 Subject: [PATCH 11/43] update changed variable name --- .github/workflows/build-windows-executable-app.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index cd8bd5f8..69410be9 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -110,10 +110,10 @@ jobs: shell: bash run: | mkdir $GITHUB_WORKSPACE/OpenMS/bld/ - ctest --output-on-failure -V -S OpenMS/tools/ci/cibuild.cmake + ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cibuild.cmake env: #OS_PREFIX_PATH: "${{ env.Qt5_DIR }}/lib/cmake;${{ env.Qt5_DIR }}" - CONTRIB_BUILD_DIRECTORY: "${{ github.workspace }}/OpenMS/contrib" + OPENMS_CONTRIB_LIBS: "${{ github.workspace }}/OpenMS/contrib" CI_PROVIDER: "GitHub-Actions" CMAKE_GENERATOR: "Ninja" SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS" From ec6b928fcad86836a38ca2cc49d38f47398f1092 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 25 Sep 2024 14:07:47 +0200 Subject: [PATCH 12/43] fix tests --- .github/workflows/build-windows-executable-app.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index 69410be9..bec4e8d9 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -148,9 +148,8 @@ jobs: - name: Test Windows shell: bash - run: $LAUNCHER ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake + run: ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake env: - LAUNCHER: "" SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS" CI_PROVIDER: "GitHub-Actions" BUILD_NAME: "${{ env.RUN_NAME }}-Win64-class-topp-${{ github.run_number }}" From 875ba468e1fbb7f53e034812448fde5945cf6605 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 25 Sep 2024 20:53:36 +0200 Subject: [PATCH 13/43] swap test and package steps --- .../workflows/build-windows-executable-app.yaml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index bec4e8d9..7d4d3f4d 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -135,6 +135,14 @@ jobs: CCACHE_COMPRESSLEVEL: 12 CCACHE_MAXSIZE: 400M + - name: Test Windows + shell: bash + run: ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake + env: + SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS" + CI_PROVIDER: "GitHub-Actions" + BUILD_NAME: "${{ env.RUN_NAME }}-Win64-class-topp-${{ github.run_number }}" + - name: Package shell: bash run: | @@ -146,14 +154,6 @@ jobs: CI_PROVIDER: "GitHub-Actions" CPACK_PACKAGE_FILE_NAME: "openms-package" - - name: Test Windows - shell: bash - run: ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake - env: - SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS" - CI_PROVIDER: "GitHub-Actions" - BUILD_NAME: "${{ env.RUN_NAME }}-Win64-class-topp-${{ github.run_number }}" - - name: Upload package as artifact uses: actions/upload-artifact@v4 with: From f8f0e8273ca438e8c181c14184b6784b9f7ecc08 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Tue, 12 Nov 2024 14:10:18 +0100 Subject: [PATCH 14/43] switch to experimental branch --- .../build-windows-executable-app.yaml | 21 ++++++++++--------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index 7d4d3f4d..32daa138 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -18,8 +18,8 @@ jobs: - name: Checkout uses: actions/checkout@v4 with: - repository: OpenMS/OpenMS - ref: release/${{ env.OPENMS_VERSION }} + repository: t0mdavid-m/OpenMS + ref: add_target_list_to_ci path: 'OpenMS' - name: Install Qt @@ -134,14 +134,15 @@ jobs: CCACHE_COMPRESS: true CCACHE_COMPRESSLEVEL: 12 CCACHE_MAXSIZE: 400M - - - name: Test Windows - shell: bash - run: ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake - env: - SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS" - CI_PROVIDER: "GitHub-Actions" - BUILD_NAME: "${{ env.RUN_NAME }}-Win64-class-topp-${{ github.run_number }}" + TARGETS_TO_BUILD: ${{ env.TOPP_TOOLS }} + + # - name: Test Windows + # shell: bash + # run: ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake + # env: + # SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS" + # CI_PROVIDER: "GitHub-Actions" + # BUILD_NAME: "${{ env.RUN_NAME }}-Win64-class-topp-${{ github.run_number }}" - name: Package shell: bash From 9f60ddcc4bd6457ac8e3961cdc0c9d7a5cc37b8d Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Thu, 14 Nov 2024 08:39:54 +0100 Subject: [PATCH 15/43] Revert "switch to experimental branch" This reverts commit f8f0e8273ca438e8c181c14184b6784b9f7ecc08. --- .../build-windows-executable-app.yaml | 21 +++++++++---------- 1 file changed, 10 insertions(+), 11 deletions(-) diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index 32daa138..7d4d3f4d 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -18,8 +18,8 @@ jobs: - name: Checkout uses: actions/checkout@v4 with: - repository: t0mdavid-m/OpenMS - ref: add_target_list_to_ci + repository: OpenMS/OpenMS + ref: release/${{ env.OPENMS_VERSION }} path: 'OpenMS' - name: Install Qt @@ -134,15 +134,14 @@ jobs: CCACHE_COMPRESS: true CCACHE_COMPRESSLEVEL: 12 CCACHE_MAXSIZE: 400M - TARGETS_TO_BUILD: ${{ env.TOPP_TOOLS }} - - # - name: Test Windows - # shell: bash - # run: ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake - # env: - # SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS" - # CI_PROVIDER: "GitHub-Actions" - # BUILD_NAME: "${{ env.RUN_NAME }}-Win64-class-topp-${{ github.run_number }}" + + - name: Test Windows + shell: bash + run: ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake + env: + SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS" + CI_PROVIDER: "GitHub-Actions" + BUILD_NAME: "${{ env.RUN_NAME }}-Win64-class-topp-${{ github.run_number }}" - name: Package shell: bash From 4bfaeeedd4438d19825026013c1cb504363fcb65 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Fri, 15 Nov 2024 10:09:12 +0100 Subject: [PATCH 16/43] disable gui --- .github/workflows/build-windows-executable-app.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index 7d4d3f4d..a727bec9 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -121,7 +121,7 @@ jobs: ENABLE_STYLE_TESTING: "OFF" ENABLE_TOPP_TESTING: "ON" ENABLE_CLASS_TESTING: "ON" - WITH_GUI: "ON" + WITH_GUI: "OFF" ADDRESS_SANITIZER: "Off" BUILD_TYPE: "Release" OPENMP: "Off" From e21c2530925816cf71721e60241468c09fd241c9 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Tue, 19 Nov 2024 16:28:31 +0100 Subject: [PATCH 17/43] fix gdpr consent --- .github/workflows/build-windows-executable-app.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index a727bec9..aaf36964 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -217,6 +217,7 @@ jobs: mv python-${{ env.PYTHON_VERSION }} streamlit_exe mv run_app.bat streamlit_exe cp -r src streamlit_exe + cp -r gdpr_consent streamlit_exe cp -r content streamlit_exe cp -r assets streamlit_exe cp -r example-data streamlit_exe From 875085c0ab97fa6988c99aaffac6b7d78fa950f5 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 12:14:02 +0100 Subject: [PATCH 18/43] add settings json --- .github/workflows/build-windows-executable-app.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index aaf36964..eb29dbf4 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -225,6 +225,7 @@ jobs: cp -r .streamlit streamlit_exe cp -r share streamlit_exe/share cp app.py streamlit_exe + cp settings.json streamlit_exe $files = $env:TOPP_TOOLS -split ' ' foreach ($file in $files) { From 865c15006568f1f1028caad7f1e5fb17b9d4c91a Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 12:41:33 +0100 Subject: [PATCH 19/43] add default json --- .github/workflows/build-windows-executable-app.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index eb29dbf4..4119868a 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -226,6 +226,7 @@ jobs: cp -r share streamlit_exe/share cp app.py streamlit_exe cp settings.json streamlit_exe + cp default-parameters.json streamlit_exe $files = $env:TOPP_TOOLS -split ' ' foreach ($file in $files) { From 910c72d254a6a2bbbcdbfa950e5a7567db278386 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 14:53:41 +0100 Subject: [PATCH 20/43] add debug --- .github/workflows/debug.yaml | 51 ++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 .github/workflows/debug.yaml diff --git a/.github/workflows/debug.yaml b/.github/workflows/debug.yaml new file mode 100644 index 00000000..f2bfffd1 --- /dev/null +++ b/.github/workflows/debug.yaml @@ -0,0 +1,51 @@ +name: Build executable for Windows +on: + push: + branches: [ "main" ] + pull_request: + branches: [ "main" ] + workflow_dispatch: +env: + OPENMS_VERSION: 3.2.0 + # Define needed TOPP tools here + TOPP_TOOLS: "FeatureFinderMetabo MetaboliteAdductDecharger SiriusExport" + +jobs: + build-executable: + runs-on: windows-latest + needs: build-openms + + env: + PYTHON_VERSION: 3.11.0 + + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: Setup python embeddable version + run: | + mkdir python-${{ env.PYTHON_VERSION }} + curl -O https://www.python.org/ftp/python/${{ env.PYTHON_VERSION }}/python-${{ env.PYTHON_VERSION }}-embed-amd64.zip + unzip python-${{ env.PYTHON_VERSION }}-embed-amd64.zip -d python-${{ env.PYTHON_VERSION }} + rm python-${{ env.PYTHON_VERSION }}-embed-amd64.zip + + - name: Install pip + run: | + curl -O https://bootstrap.pypa.io/get-pip.py + ./python-${{ env.PYTHON_VERSION }}/python get-pip.py --no-warn-script-location + rm get-pip.py + + - name: Uncomment 'import site' in python311._pth file + run: | + sed -i 's/#import site/import site/' python-${{ env.PYTHON_VERSION }}/python311._pth + + - name: Install Required Packages + run: .\python-${{ env.PYTHON_VERSION }}\python -m pip install --force-reinstall -r requirements.txt --no-warn-script-location + + - name: Create run_app.bat file + run: | + echo '@echo off' > run_app.bat + echo '.\\python-${{ env.PYTHON_VERSION }}\\python -m streamlit run app.py local' >> run_app.bat + + - name: List Root Folder + run: ls -al \ No newline at end of file From f746c4b9bac393e8299861697a23e59423e99fdf Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 14:54:30 +0100 Subject: [PATCH 21/43] update name --- .github/workflows/debug.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/debug.yaml b/.github/workflows/debug.yaml index f2bfffd1..37feaccc 100644 --- a/.github/workflows/debug.yaml +++ b/.github/workflows/debug.yaml @@ -1,4 +1,4 @@ -name: Build executable for Windows +name: Debug on: push: branches: [ "main" ] From ddaa5e5679b0262a29ed167606cd064266fd5c60 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 14:55:59 +0100 Subject: [PATCH 22/43] update run conditions --- .github/workflows/debug.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/debug.yaml b/.github/workflows/debug.yaml index 37feaccc..12ad6443 100644 --- a/.github/workflows/debug.yaml +++ b/.github/workflows/debug.yaml @@ -1,9 +1,11 @@ name: Debug on: push: - branches: [ "main" ] + branches: + - "**" pull_request: - branches: [ "main" ] + branches: + - "**" workflow_dispatch: env: OPENMS_VERSION: 3.2.0 From c12a2a796cc123884e261165f72c236bdcdef12c Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 14:56:59 +0100 Subject: [PATCH 23/43] remove dependency --- .github/workflows/debug.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/debug.yaml b/.github/workflows/debug.yaml index 12ad6443..e0b6f9d5 100644 --- a/.github/workflows/debug.yaml +++ b/.github/workflows/debug.yaml @@ -15,7 +15,6 @@ env: jobs: build-executable: runs-on: windows-latest - needs: build-openms env: PYTHON_VERSION: 3.11.0 From afd759904e0b329a0cc9302dbaa4531806d6be94 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 14:59:33 +0100 Subject: [PATCH 24/43] fix pattern --- .github/workflows/debug.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/debug.yaml b/.github/workflows/debug.yaml index e0b6f9d5..81a2a55d 100644 --- a/.github/workflows/debug.yaml +++ b/.github/workflows/debug.yaml @@ -2,10 +2,10 @@ name: Debug on: push: branches: - - "**" + - "*" pull_request: branches: - - "**" + - "*" workflow_dispatch: env: OPENMS_VERSION: 3.2.0 From 8c5525e3f45c955e1a67b6503772bb8de1fef460 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 15:00:26 +0100 Subject: [PATCH 25/43] fix --- .github/workflows/debug.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/debug.yaml b/.github/workflows/debug.yaml index 81a2a55d..0374c8d1 100644 --- a/.github/workflows/debug.yaml +++ b/.github/workflows/debug.yaml @@ -1,11 +1,9 @@ name: Debug on: push: - branches: - - "*" + branches: [ "main" ] pull_request: - branches: - - "*" + branches: [ "main" ] workflow_dispatch: env: OPENMS_VERSION: 3.2.0 From c0f91e74f34f409f871dcb6c1555b3c893a8970c Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 15:03:23 +0100 Subject: [PATCH 26/43] should run now --- .github/workflows/debug.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/debug.yaml b/.github/workflows/debug.yaml index 0374c8d1..6780bb4b 100644 --- a/.github/workflows/debug.yaml +++ b/.github/workflows/debug.yaml @@ -1,7 +1,7 @@ name: Debug on: push: - branches: [ "main" ] + branches: [ "install_all_dependencies" ] pull_request: branches: [ "main" ] workflow_dispatch: From f9eb657a3e57a027b427b19c9e2c62e6d8c4aa4c Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 15:04:52 +0100 Subject: [PATCH 27/43] fix syntax --- .github/workflows/debug.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/debug.yaml b/.github/workflows/debug.yaml index 6780bb4b..320b0bb6 100644 --- a/.github/workflows/debug.yaml +++ b/.github/workflows/debug.yaml @@ -47,4 +47,5 @@ jobs: echo '.\\python-${{ env.PYTHON_VERSION }}\\python -m streamlit run app.py local' >> run_app.bat - name: List Root Folder - run: ls -al \ No newline at end of file + run: | + ls -al \ No newline at end of file From ee6ac95aca15756445fdc075718ee11b7a47d957 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 15:07:08 +0100 Subject: [PATCH 28/43] remember that we are on windows --- .github/workflows/debug.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/debug.yaml b/.github/workflows/debug.yaml index 320b0bb6..c22738fe 100644 --- a/.github/workflows/debug.yaml +++ b/.github/workflows/debug.yaml @@ -48,4 +48,4 @@ jobs: - name: List Root Folder run: | - ls -al \ No newline at end of file + dir \ No newline at end of file From fc3138fe3c955669f8c72cab85219f34cfe82ba8 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 15:19:16 +0100 Subject: [PATCH 29/43] update as artifact --- .github/workflows/debug.yaml | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/.github/workflows/debug.yaml b/.github/workflows/debug.yaml index c22738fe..cd9e02be 100644 --- a/.github/workflows/debug.yaml +++ b/.github/workflows/debug.yaml @@ -48,4 +48,15 @@ jobs: - name: List Root Folder run: | - dir \ No newline at end of file + dir + + - name: Move All Files to Folder + run: | + mkdir artifact_folder + move * artifact_folder + + - name: Upload Artifact + uses: actions/upload-artifact@v3 + with: + name: my-artifact + path: artifact_folder \ No newline at end of file From ff81a6fa6c61ca06945fd80a5c58a7f507f33a3e Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 15:19:44 +0100 Subject: [PATCH 30/43] downgrade pyopenms --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index c401482d..9da58fda 100644 --- a/requirements.txt +++ b/requirements.txt @@ -2,7 +2,7 @@ # note that it is much more restricted in terms of installing third-parties / etc. # preferably use the batteries included or simple docker file for local hosting streamlit>=1.38.0 -pyopenms==3.2.0 +pyopenms==3.1.0 numpy==1.26.4 # pandas and numpy are dependencies of pyopenms, however, pyopenms needs numpy<=1.26.4 plotly==5.22.0 captcha==0.5.0 From 0f21a8f156906438279d5d1b33e16477b1445c24 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 15:22:06 +0100 Subject: [PATCH 31/43] use powershell --- .github/workflows/debug.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/debug.yaml b/.github/workflows/debug.yaml index cd9e02be..cb00bea9 100644 --- a/.github/workflows/debug.yaml +++ b/.github/workflows/debug.yaml @@ -51,9 +51,10 @@ jobs: dir - name: Move All Files to Folder + shell: powershell run: | - mkdir artifact_folder - move * artifact_folder + New-Item -ItemType Directory -Force -Path artifact_folder + Get-ChildItem -File | ForEach-Object { Move-Item $_.FullName artifact_folder } - name: Upload Artifact uses: actions/upload-artifact@v3 From f48316923287239f6dee663ba21612b371b56653 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 15:24:23 +0100 Subject: [PATCH 32/43] include folders --- .github/workflows/debug.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/debug.yaml b/.github/workflows/debug.yaml index cb00bea9..aee5c9f6 100644 --- a/.github/workflows/debug.yaml +++ b/.github/workflows/debug.yaml @@ -51,10 +51,9 @@ jobs: dir - name: Move All Files to Folder - shell: powershell run: | - New-Item -ItemType Directory -Force -Path artifact_folder - Get-ChildItem -File | ForEach-Object { Move-Item $_.FullName artifact_folder } + mkdir artifact_folder + for %f in (*) do if not "%f"=="artifact_folder" move "%f" artifact_folder - name: Upload Artifact uses: actions/upload-artifact@v3 From e907c87f91bf7514eeec825210106ed579112fbd Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 15:26:51 +0100 Subject: [PATCH 33/43] use powershell again --- .github/workflows/debug.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/workflows/debug.yaml b/.github/workflows/debug.yaml index aee5c9f6..181f294e 100644 --- a/.github/workflows/debug.yaml +++ b/.github/workflows/debug.yaml @@ -51,9 +51,13 @@ jobs: dir - name: Move All Files to Folder + shell: powershell run: | - mkdir artifact_folder - for %f in (*) do if not "%f"=="artifact_folder" move "%f" artifact_folder + New-Item -ItemType Directory -Force -Path artifact_folder + Get-ChildItem -Path . -Exclude artifact_folder | ForEach-Object { + Move-Item -Path $_.FullName -Destination artifact_folder + } + - name: Upload Artifact uses: actions/upload-artifact@v3 From f70c3bddc557ff3cfd51d3724bdd0aece84d3116 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 15:58:03 +0100 Subject: [PATCH 34/43] fix weird pyopenms bug --- .github/workflows/debug.yaml | 66 ------------------------------------ app.py | 2 ++ requirements.txt | 2 +- 3 files changed, 3 insertions(+), 67 deletions(-) delete mode 100644 .github/workflows/debug.yaml diff --git a/.github/workflows/debug.yaml b/.github/workflows/debug.yaml deleted file mode 100644 index 181f294e..00000000 --- a/.github/workflows/debug.yaml +++ /dev/null @@ -1,66 +0,0 @@ -name: Debug -on: - push: - branches: [ "install_all_dependencies" ] - pull_request: - branches: [ "main" ] - workflow_dispatch: -env: - OPENMS_VERSION: 3.2.0 - # Define needed TOPP tools here - TOPP_TOOLS: "FeatureFinderMetabo MetaboliteAdductDecharger SiriusExport" - -jobs: - build-executable: - runs-on: windows-latest - - env: - PYTHON_VERSION: 3.11.0 - - steps: - - name: Checkout - uses: actions/checkout@v4 - - - name: Setup python embeddable version - run: | - mkdir python-${{ env.PYTHON_VERSION }} - curl -O https://www.python.org/ftp/python/${{ env.PYTHON_VERSION }}/python-${{ env.PYTHON_VERSION }}-embed-amd64.zip - unzip python-${{ env.PYTHON_VERSION }}-embed-amd64.zip -d python-${{ env.PYTHON_VERSION }} - rm python-${{ env.PYTHON_VERSION }}-embed-amd64.zip - - - name: Install pip - run: | - curl -O https://bootstrap.pypa.io/get-pip.py - ./python-${{ env.PYTHON_VERSION }}/python get-pip.py --no-warn-script-location - rm get-pip.py - - - name: Uncomment 'import site' in python311._pth file - run: | - sed -i 's/#import site/import site/' python-${{ env.PYTHON_VERSION }}/python311._pth - - - name: Install Required Packages - run: .\python-${{ env.PYTHON_VERSION }}\python -m pip install --force-reinstall -r requirements.txt --no-warn-script-location - - - name: Create run_app.bat file - run: | - echo '@echo off' > run_app.bat - echo '.\\python-${{ env.PYTHON_VERSION }}\\python -m streamlit run app.py local' >> run_app.bat - - - name: List Root Folder - run: | - dir - - - name: Move All Files to Folder - shell: powershell - run: | - New-Item -ItemType Directory -Force -Path artifact_folder - Get-ChildItem -Path . -Exclude artifact_folder | ForEach-Object { - Move-Item -Path $_.FullName -Destination artifact_folder - } - - - - name: Upload Artifact - uses: actions/upload-artifact@v3 - with: - name: my-artifact - path: artifact_folder \ No newline at end of file diff --git a/app.py b/app.py index 907c581c..2f863cde 100644 --- a/app.py +++ b/app.py @@ -1,5 +1,7 @@ import streamlit as st from pathlib import Path +# For some reason the windows version only works if this is imported here +import pyopenms if __name__ == '__main__': pages = { diff --git a/requirements.txt b/requirements.txt index 9da58fda..c401482d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -2,7 +2,7 @@ # note that it is much more restricted in terms of installing third-parties / etc. # preferably use the batteries included or simple docker file for local hosting streamlit>=1.38.0 -pyopenms==3.1.0 +pyopenms==3.2.0 numpy==1.26.4 # pandas and numpy are dependencies of pyopenms, however, pyopenms needs numpy<=1.26.4 plotly==5.22.0 captcha==0.5.0 From 1ca01861f7730260350a319db619183672786223 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 15:59:53 +0100 Subject: [PATCH 35/43] move files outside bin --- .github/workflows/build-windows-executable-app.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index 4119868a..8d0a1e3d 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -221,7 +221,7 @@ jobs: cp -r content streamlit_exe cp -r assets streamlit_exe cp -r example-data streamlit_exe - cp openms-bin/*.dll streamlit_exe/bin/ + cp openms-bin/*.dll streamlit_exe cp -r .streamlit streamlit_exe cp -r share streamlit_exe/share cp app.py streamlit_exe @@ -230,7 +230,7 @@ jobs: $files = $env:TOPP_TOOLS -split ' ' foreach ($file in $files) { - Copy-Item "openms-bin/${file}.exe" -Destination "streamlit_exe/bin/${file}.exe" + Copy-Item "openms-bin/${file}.exe" -Destination "streamlit_exe/${file}.exe" } - name: Delete OpenMS bin artifact From 2ac9ab94b8c1e745b6ef168b84d02e97f82e87c7 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Wed, 20 Nov 2024 16:08:49 +0100 Subject: [PATCH 36/43] adjust topp tools --- .github/workflows/build-windows-executable-app.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index 8d0a1e3d..8cad429b 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -8,7 +8,7 @@ on: env: OPENMS_VERSION: 3.2.0 # Define needed TOPP tools here - TOPP_TOOLS: "FeatureFinderMetabo MetaboliteAdductDecharger SiriusExport" + TOPP_TOOLS: "FeatureFinderMetabo FeatureLinkerUnlabeledKD SiriusExport" jobs: build-openms: From 9585b47bd766fdf391146892ad313a6d5551f82a Mon Sep 17 00:00:00 2001 From: Arslan Siraj Date: Wed, 20 Nov 2024 22:20:45 +0100 Subject: [PATCH 37/43] add docs folder to win installer folder --- .github/workflows/build-windows-executable-app.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index 8cad429b..309201ad 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -219,6 +219,7 @@ jobs: cp -r src streamlit_exe cp -r gdpr_consent streamlit_exe cp -r content streamlit_exe + cp -r docs streamlit_exe cp -r assets streamlit_exe cp -r example-data streamlit_exe cp openms-bin/*.dll streamlit_exe From 3e99aa566646a959d98e60521572f5a7ed8d3494 Mon Sep 17 00:00:00 2001 From: Arslan Siraj Date: Wed, 20 Nov 2024 22:50:32 +0100 Subject: [PATCH 38/43] Update build-windows-executable-app-with-pyinstaller.yaml:: docs folder copy --- .../workflows/build-windows-executable-app-with-pyinstaller.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml index c7967163..63e85f2b 100644 --- a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml +++ b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml @@ -228,6 +228,7 @@ jobs: cp -r .streamlit dist/.streamlit cp -r content dist/content + cp -r docs dist/docs cp -r src dist/src cp -r assets dist/assets cp -r example-data dist/example-data From 5599c42fb8d76b34555516e9e0e03dd99d7ff294 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Thu, 21 Nov 2024 09:44:12 +0100 Subject: [PATCH 39/43] remove bin and equalize with pyinstaller --- ...ndows-executable-app-with-pyinstaller.yaml | 30 +++++++++++-------- .../build-windows-executable-app.yaml | 1 - 2 files changed, 17 insertions(+), 14 deletions(-) diff --git a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml index 63e85f2b..af504ad0 100644 --- a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml +++ b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml @@ -223,22 +223,26 @@ jobs: - name: Copy everything to dist directory run: | - mkdir dist - mkdir dist/bin - - cp -r .streamlit dist/.streamlit - cp -r content dist/content - cp -r docs dist/docs - cp -r src dist/src - cp -r assets dist/assets - cp -r example-data dist/example-data - cp openms-bin/*.dll streamlit_exe/bin/ - cp -r share dist/share - cp app.py dist/ + mkdir streamlit_exe + + mv python-${{ env.PYTHON_VERSION }} streamlit_exe + mv run_app.bat streamlit_exe + cp -r src streamlit_exe + cp -r gdpr_consent streamlit_exe + cp -r content streamlit_exe + cp -r docs streamlit_exe + cp -r assets streamlit_exe + cp -r example-data streamlit_exe + cp openms-bin/*.dll streamlit_exe + cp -r .streamlit streamlit_exe + cp -r share streamlit_exe/share + cp app.py streamlit_exe + cp settings.json streamlit_exe + cp default-parameters.json streamlit_exe $files = $env:TOPP_TOOLS -split ' ' foreach ($file in $files) { - Copy-Item "openms-bin/${file}.exe" -Destination "dist/bin/${file}.exe" + Copy-Item "openms-bin/${file}.exe" -Destination "streamlit_exe/${file}.exe" } - name: Modify .spec file diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index 309201ad..f92e3ae3 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -212,7 +212,6 @@ jobs: - name: Create All-in-one executable folder run: | mkdir streamlit_exe - mkdir streamlit_exe/bin mv python-${{ env.PYTHON_VERSION }} streamlit_exe mv run_app.bat streamlit_exe From 19fd5ef13de4c79c71e2565a231d272773f7c22a Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Thu, 21 Nov 2024 09:59:30 +0100 Subject: [PATCH 40/43] remove gdpr for local files --- .../build-windows-executable-app-with-pyinstaller.yaml | 1 - .github/workflows/build-windows-executable-app.yaml | 1 - src/common/captcha_.py | 4 +--- 3 files changed, 1 insertion(+), 5 deletions(-) diff --git a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml index af504ad0..43cd29a8 100644 --- a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml +++ b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml @@ -228,7 +228,6 @@ jobs: mv python-${{ env.PYTHON_VERSION }} streamlit_exe mv run_app.bat streamlit_exe cp -r src streamlit_exe - cp -r gdpr_consent streamlit_exe cp -r content streamlit_exe cp -r docs streamlit_exe cp -r assets streamlit_exe diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index f92e3ae3..2305e59b 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -216,7 +216,6 @@ jobs: mv python-${{ env.PYTHON_VERSION }} streamlit_exe mv run_app.bat streamlit_exe cp -r src streamlit_exe - cp -r gdpr_consent streamlit_exe cp -r content streamlit_exe cp -r docs streamlit_exe cp -r assets streamlit_exe diff --git a/src/common/captcha_.py b/src/common/captcha_.py index 5788d08e..b8dfaa68 100644 --- a/src/common/captcha_.py +++ b/src/common/captcha_.py @@ -10,9 +10,6 @@ import os -consent_component = st_components.declare_component("gdpr_consent", path=Path("gdpr_consent")) - - def delete_all_pages(main_script_path_str: str) -> None: """ Delete all pages except the main page from an app's configuration. @@ -203,6 +200,7 @@ def captcha_control(): ga = st.session_state.settings['analytics']['google-analytics']['enabled'] pp = st.session_state.settings['analytics']['piwik-pro']['enabled'] if (ga or pp) and (st.session_state.tracking_consent is None): + consent_component = st_components.declare_component("gdpr_consent", path=Path("gdpr_consent")) with st.spinner(): # Ask for consent st.session_state.tracking_consent = consent_component( From 01fd5151699df0f6e638c11d3ba2db410d261731 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Thu, 21 Nov 2024 10:01:27 +0100 Subject: [PATCH 41/43] ensure that offline deployment is selected --- .../build-windows-executable-app-with-pyinstaller.yaml | 3 +++ .github/workflows/build-windows-executable-app.yaml | 6 +++++- 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml index 43cd29a8..03b339cc 100644 --- a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml +++ b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml @@ -220,6 +220,9 @@ jobs: call myenv\Scripts\activate.bat pyinstaller --onefile --additional-hooks-dir ./hooks run_app.py --clean + - name: Set to offline deployment + run: | + jq '.online_deployment = true' settings.json > tmp.json && mv tmp.json settings.json - name: Copy everything to dist directory run: | diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index 2305e59b..1f37bd73 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -208,7 +208,11 @@ jobs: run: | echo '@echo off' > run_app.bat echo '.\\python-${{ env.PYTHON_VERSION }}\\python -m streamlit run app.py local' >> run_app.bat - + + - name: Set to offline deployment + run: | + jq '.online_deployment = true' settings.json > tmp.json && mv tmp.json settings.json + - name: Create All-in-one executable folder run: | mkdir streamlit_exe From 9d67f285c561d66ca7608c3122b1810d0f341dc1 Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Thu, 21 Nov 2024 10:02:10 +0100 Subject: [PATCH 42/43] fixup! remove gdpr for local files --- .../build-windows-executable-app-with-pyinstaller.yaml | 2 +- .github/workflows/build-windows-executable-app.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml index 03b339cc..c907b515 100644 --- a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml +++ b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml @@ -222,7 +222,7 @@ jobs: - name: Set to offline deployment run: | - jq '.online_deployment = true' settings.json > tmp.json && mv tmp.json settings.json + jq '.online_deployment = false' settings.json > tmp.json && mv tmp.json settings.json - name: Copy everything to dist directory run: | diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index 1f37bd73..de814489 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -211,7 +211,7 @@ jobs: - name: Set to offline deployment run: | - jq '.online_deployment = true' settings.json > tmp.json && mv tmp.json settings.json + jq '.online_deployment = false' settings.json > tmp.json && mv tmp.json settings.json - name: Create All-in-one executable folder run: | From a7ba5dd08012553a159977bc96129c5a9d6e80be Mon Sep 17 00:00:00 2001 From: Tom David Mueller Date: Thu, 21 Nov 2024 10:35:07 +0100 Subject: [PATCH 43/43] adjust settings mod to powershell --- .../build-windows-executable-app-with-pyinstaller.yaml | 4 +++- .github/workflows/build-windows-executable-app.yaml | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml index c907b515..42646e82 100644 --- a/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml +++ b/.github/workflows/build-windows-executable-app-with-pyinstaller.yaml @@ -222,7 +222,9 @@ jobs: - name: Set to offline deployment run: | - jq '.online_deployment = false' settings.json > tmp.json && mv tmp.json settings.json + $content = Get-Content -Raw settings.json | ConvertFrom-Json + $content.online_deployment = $false + $content | ConvertTo-Json -Depth 100 | Set-Content settings.json - name: Copy everything to dist directory run: | diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml index de814489..da8e75fa 100644 --- a/.github/workflows/build-windows-executable-app.yaml +++ b/.github/workflows/build-windows-executable-app.yaml @@ -211,7 +211,9 @@ jobs: - name: Set to offline deployment run: | - jq '.online_deployment = false' settings.json > tmp.json && mv tmp.json settings.json + $content = Get-Content -Raw settings.json | ConvertFrom-Json + $content.online_deployment = $false + $content | ConvertTo-Json -Depth 100 | Set-Content settings.json - name: Create All-in-one executable folder run: |