From 1db6dd8f749abbbe45a41b85004a2c3dea000a90 Mon Sep 17 00:00:00 2001 From: pradal Date: Mon, 5 Feb 2024 08:26:57 +0100 Subject: [PATCH 01/22] Update conda to fix errors in CI --- conda/conda_build_config.yml | 44 ++++++++++++++++++++++++++++++++++++ conda/meta.yaml | 21 +++++++++-------- 2 files changed, 56 insertions(+), 9 deletions(-) create mode 100644 conda/conda_build_config.yml diff --git a/conda/conda_build_config.yml b/conda/conda_build_config.yml new file mode 100644 index 0000000..0ba9e83 --- /dev/null +++ b/conda/conda_build_config.yml @@ -0,0 +1,44 @@ +# from conda-forge-pinning +c_compiler: + - gcc # [linux] + - clang # [osx] + - vs2019 # [win and x86_64] + - vs2022 # [win and arm64] +c_compiler_version: # [unix] + - 12 # [linux] + - 16 # [osx] + - 10 # [os.environ.get("CF_CUDA_ENABLED", "False") == "True" and linux] + - 11 # [os.environ.get("CF_CUDA_ENABLED", "False") == "True" and linux] +cxx_compiler: + - gxx # [linux] + - clangxx # [osx] + - vs2019 # [win and x86_64] + - vs2022 # [win and arm64] +cxx_compiler_version: # [unix] + - 12 # [linux] + - 16 # [osx] + - 10 # [os.environ.get("CF_CUDA_ENABLED", "False") == "True" and linux] + - 11 # [os.environ.get("CF_CUDA_ENABLED", "False") == "True" and linux] +m2w64_c_compiler: # [win] + - m2w64-toolchain # [win] +m2w64_cxx_compiler: # [win] + - m2w64-toolchain # [win] +# from conda-forge-pinning +c_compiler: + - gcc # [linux] + - clang # [osx] + - m2w64-toolchain # [win] +c_compiler_version: # [unix] + - 12 # [linux] + - 16 # [osx] + - 10 # [os.environ.get("CF_CUDA_ENABLED", "False") == "True" and linux] + - 11 # [os.environ.get("CF_CUDA_ENABLED", "False") == "True" and linux] +cxx_compiler: + - gxx # [linux] + - clangxx # [osx] + - m2w64-toolchain # [win] +cxx_compiler_version: # [unix] + - 12 # [linux] + - 16 # [osx] + - 10 # [os.environ.get("CF_CUDA_ENABLED", "False") == "True" and linux] + - 11 # [os.environ.get("CF_CUDA_ENABLED", "False") == "True" and linux] diff --git a/conda/meta.yaml b/conda/meta.yaml index e6bb198..d8d5022 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -1,3 +1,5 @@ +{% set native = 'm2w64-' if win else '' %} + package: name: openalea.phenomenal version: "1.9.2" @@ -10,24 +12,25 @@ build: preserve_egg_dir: True string: phenomenal script: - - {{ PYTHON }} setup.py install #--single-version-externally-managed --record record.txt + - script: pip install . requirements: + host: + - python x.x + - setuptools + - cython + - numpy + - scipy build: - - {{ compiler('c') }} - - {{ compiler("cxx") }} + - {{ compiler('c') }} # [unix] + - {{ compiler("cxx") }} # [unix] + - m2w64-toolchain # [win] - python - setuptools - numpy - cython - host: - - python - - setuptools - - cython - - numpy - - scipy run: - python From 966583cff3afdf541e3b6b000647c2eee32d7fc6 Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 16:08:11 +0100 Subject: [PATCH 02/22] Update conda_build_config.yml Remove duplicate information --- conda/conda_build_config.yml | 21 --------------------- 1 file changed, 21 deletions(-) diff --git a/conda/conda_build_config.yml b/conda/conda_build_config.yml index 0ba9e83..fa55ad0 100644 --- a/conda/conda_build_config.yml +++ b/conda/conda_build_config.yml @@ -1,29 +1,8 @@ # from conda-forge-pinning -c_compiler: - - gcc # [linux] - - clang # [osx] - - vs2019 # [win and x86_64] - - vs2022 # [win and arm64] -c_compiler_version: # [unix] - - 12 # [linux] - - 16 # [osx] - - 10 # [os.environ.get("CF_CUDA_ENABLED", "False") == "True" and linux] - - 11 # [os.environ.get("CF_CUDA_ENABLED", "False") == "True" and linux] -cxx_compiler: - - gxx # [linux] - - clangxx # [osx] - - vs2019 # [win and x86_64] - - vs2022 # [win and arm64] -cxx_compiler_version: # [unix] - - 12 # [linux] - - 16 # [osx] - - 10 # [os.environ.get("CF_CUDA_ENABLED", "False") == "True" and linux] - - 11 # [os.environ.get("CF_CUDA_ENABLED", "False") == "True" and linux] m2w64_c_compiler: # [win] - m2w64-toolchain # [win] m2w64_cxx_compiler: # [win] - m2w64-toolchain # [win] -# from conda-forge-pinning c_compiler: - gcc # [linux] - clang # [osx] From 8ce0c0e8b2ac929ed23f2fa66377f98a111a1124 Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 16:14:23 +0100 Subject: [PATCH 03/22] Update meta.yaml --- conda/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda/meta.yaml b/conda/meta.yaml index d8d5022..bfc490c 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -12,7 +12,7 @@ build: preserve_egg_dir: True string: phenomenal script: - - script: pip install . + - script: python setup.py install requirements: host: From d2f6d5c4d2f1d66d7066a0774341f2178031e72e Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 16:21:46 +0100 Subject: [PATCH 04/22] Update meta.yaml Fix syntax error --- conda/meta.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/conda/meta.yaml b/conda/meta.yaml index bfc490c..714cebb 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -11,8 +11,7 @@ build: number: 0 preserve_egg_dir: True string: phenomenal - script: - - script: python setup.py install + script: pip install . requirements: host: From f9c568fa9bf8a1145f410441ee3a6846dc4952c0 Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 16:37:24 +0100 Subject: [PATCH 05/22] Update meta.yaml Manage Python version with x.x in both run and host --- conda/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conda/meta.yaml b/conda/meta.yaml index 714cebb..728735c 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -25,14 +25,14 @@ requirements: - {{ compiler('c') }} # [unix] - {{ compiler("cxx") }} # [unix] - m2w64-toolchain # [win] - - python + - python - setuptools - numpy - cython run: - - python + - python x.x - numpy - cython - numba From dfa8b5ebca67babaaa4494627780ac6d464fb34d Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 16:51:42 +0100 Subject: [PATCH 06/22] Update meta.yaml --- conda/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda/meta.yaml b/conda/meta.yaml index 728735c..19d00e9 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -11,7 +11,7 @@ build: number: 0 preserve_egg_dir: True string: phenomenal - script: pip install . + script: python setup.py install requirements: host: From 7753831cd7372b004e385d7bd49a839a9d9551f5 Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 17:28:02 +0100 Subject: [PATCH 07/22] Update meta.yaml --- conda/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda/meta.yaml b/conda/meta.yaml index 19d00e9..8205062 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -11,7 +11,7 @@ build: number: 0 preserve_egg_dir: True string: phenomenal - script: python setup.py install + script: {{PYTHON}} setup.py install requirements: host: From 7123bb7e00e79d9f45e6c7ef1062abdbdbeb9abc Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 17:42:35 +0100 Subject: [PATCH 08/22] Update conda_build_config.yml Update compilers flags for windows --- conda/conda_build_config.yml | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/conda/conda_build_config.yml b/conda/conda_build_config.yml index fa55ad0..4dd09ce 100644 --- a/conda/conda_build_config.yml +++ b/conda/conda_build_config.yml @@ -1,12 +1,9 @@ # from conda-forge-pinning -m2w64_c_compiler: # [win] - - m2w64-toolchain # [win] -m2w64_cxx_compiler: # [win] - - m2w64-toolchain # [win] c_compiler: - gcc # [linux] - clang # [osx] - - m2w64-toolchain # [win] + - vs2019 # [win and x86_64] + - vs2022 # [win and arm64] c_compiler_version: # [unix] - 12 # [linux] - 16 # [osx] @@ -15,7 +12,8 @@ c_compiler_version: # [unix] cxx_compiler: - gxx # [linux] - clangxx # [osx] - - m2w64-toolchain # [win] + - vs2019 # [win and x86_64] + - vs2022 # [win and arm64] cxx_compiler_version: # [unix] - 12 # [linux] - 16 # [osx] From cf964ebacd1e8924572dffe1f73f007099a81ebb Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 17:43:28 +0100 Subject: [PATCH 09/22] Update meta.yaml --- conda/meta.yaml | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/conda/meta.yaml b/conda/meta.yaml index 8205062..030b2dd 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -1,5 +1,3 @@ -{% set native = 'm2w64-' if win else '' %} - package: name: openalea.phenomenal version: "1.9.2" @@ -22,9 +20,8 @@ requirements: - scipy build: - - {{ compiler('c') }} # [unix] - - {{ compiler("cxx") }} # [unix] - - m2w64-toolchain # [win] + - {{ compiler('c') }} + - {{ compiler("cxx") }} - python - setuptools - numpy From 08a737e7f72775ca31cb9e5e3ae5ab59f7bc436b Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 18:06:03 +0100 Subject: [PATCH 10/22] Update meta.yaml remove cython as runtime requirement --- conda/meta.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/conda/meta.yaml b/conda/meta.yaml index 030b2dd..56758fb 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -31,7 +31,6 @@ requirements: run: - python x.x - numpy - - cython - numba - scipy - scikit-image From f6b0d020c9c9be8b16acb7150e22768298c51e06 Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 18:21:00 +0100 Subject: [PATCH 11/22] Update meta.yaml Update for mac --- conda/meta.yaml | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/conda/meta.yaml b/conda/meta.yaml index 56758fb..779f2e0 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -14,10 +14,8 @@ build: requirements: host: - python x.x - - setuptools - - cython - - numpy - - scipy + - numpy x.x + - scipy x.x build: - {{ compiler('c') }} @@ -30,9 +28,9 @@ requirements: run: - python x.x - - numpy + - numpy x.x - numba - - scipy + - scipy x.x - scikit-image - scikit-learn - networkx From 5cff5ddb2b47481213ac0c665232e89db2b0f747 Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 18:27:01 +0100 Subject: [PATCH 12/22] Update meta.yaml --- conda/meta.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/conda/meta.yaml b/conda/meta.yaml index 779f2e0..c29139c 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -15,7 +15,6 @@ requirements: host: - python x.x - numpy x.x - - scipy x.x build: - {{ compiler('c') }} @@ -30,7 +29,7 @@ requirements: - python x.x - numpy x.x - numba - - scipy x.x + - scipy - scikit-image - scikit-learn - networkx From dcd78b7cb034dc2c250c6ea31773e4c1150668e2 Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 19:30:48 +0100 Subject: [PATCH 13/22] Update meta.yaml Add cython as host --- conda/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/conda/meta.yaml b/conda/meta.yaml index c29139c..87eea09 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -15,6 +15,7 @@ requirements: host: - python x.x - numpy x.x + - cython build: - {{ compiler('c') }} From 45da1335838b1060ce867c2a5fc751f06c3fe71f Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 20:27:05 +0100 Subject: [PATCH 14/22] Update skan version --- conda/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda/meta.yaml b/conda/meta.yaml index 87eea09..1149cfd 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -38,7 +38,7 @@ requirements: - opencv!=4.1.2 [osx] - matplotlib - vtk - - skan=0.10 + - skan>=0.10 - pywin32 [win] test: From 510ea170f4958501bd9e8eaae081799c67a525a7 Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 20:29:51 +0100 Subject: [PATCH 15/22] Update meta.yaml --- conda/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda/meta.yaml b/conda/meta.yaml index 1149cfd..5b0a791 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -35,7 +35,7 @@ requirements: - scikit-learn - networkx - opencv [win or linux] - - opencv!=4.1.2 [osx] + - opencv >4.1.2 [osx] - matplotlib - vtk - skan>=0.10 From 401fc74acfdf1d51e979314445f10f1006251829 Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 20:56:50 +0100 Subject: [PATCH 16/22] Update meta.yaml --- conda/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conda/meta.yaml b/conda/meta.yaml index 5b0a791..694b466 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -15,7 +15,6 @@ requirements: host: - python x.x - numpy x.x - - cython build: - {{ compiler('c') }} @@ -29,6 +28,7 @@ requirements: run: - python x.x - numpy x.x + - cython - numba - scipy - scikit-image From 4335cb558277cf3ab9f28e301da47187ab434333 Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 21:04:48 +0100 Subject: [PATCH 17/22] Update meta.yaml --- conda/meta.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/conda/meta.yaml b/conda/meta.yaml index 694b466..c78eee0 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -15,15 +15,13 @@ requirements: host: - python x.x - numpy x.x + - cython build: - {{ compiler('c') }} - {{ compiler("cxx") }} - python - setuptools - - numpy - - cython - run: - python x.x From d0f18d3c7fe2b49e07a37f34e84b61371712cd05 Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 21:20:06 +0100 Subject: [PATCH 18/22] Update meta.yaml --- conda/meta.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/conda/meta.yaml b/conda/meta.yaml index c78eee0..becdabf 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -13,8 +13,9 @@ build: requirements: host: - - python x.x - - numpy x.x + - python + - numpy + - scipy - cython build: @@ -22,6 +23,9 @@ requirements: - {{ compiler("cxx") }} - python - setuptools + - numpy + - scipy + - cython run: - python x.x From 28fd0819f5a0d632e9e7cb18017ff6b0a684cf9c Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 21:44:23 +0100 Subject: [PATCH 19/22] Update setup.py --- setup.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index f80fe57..ae7b70f 100644 --- a/setup.py +++ b/setup.py @@ -68,7 +68,7 @@ packages=packages, package_dir={'': 'src'}, zip_safe=False, - ext_modules=cythonize(extentions), + ext_modules=cythonize(extentions, language_level = "3"), entry_points={ "wralea": ["openalea.phenomenal = openalea.phenomenal_wralea", ], @@ -76,4 +76,4 @@ # See MANIFEST.in include_package_data=True, - ) \ No newline at end of file + ) From 3985aa3f0d8dff0bfb5c4b616aa29924af490390 Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 22:03:32 +0100 Subject: [PATCH 20/22] Update conda-package-build.yml --- .github/workflows/conda-package-build.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/conda-package-build.yml b/.github/workflows/conda-package-build.yml index 235e496..a8cd844 100644 --- a/.github/workflows/conda-package-build.yml +++ b/.github/workflows/conda-package-build.yml @@ -13,5 +13,7 @@ on: jobs: build: uses: openalea/github-action-conda-build/.github/workflows/conda-package-build.yml@main + with: + conda: mamba secrets: - anaconda_token: ${{ secrets.ANACONDA_TOKEN }} \ No newline at end of file + anaconda_token: ${{ secrets.ANACONDA_TOKEN }} From a2809c8da4cc9892a4ac35982a312a71dfad93e5 Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 22:06:25 +0100 Subject: [PATCH 21/22] Update conda-package-build.yml --- .github/workflows/conda-package-build.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/conda-package-build.yml b/.github/workflows/conda-package-build.yml index a8cd844..2a6cfa5 100644 --- a/.github/workflows/conda-package-build.yml +++ b/.github/workflows/conda-package-build.yml @@ -13,7 +13,5 @@ on: jobs: build: uses: openalea/github-action-conda-build/.github/workflows/conda-package-build.yml@main - with: - conda: mamba secrets: anaconda_token: ${{ secrets.ANACONDA_TOKEN }} From 21e00708dccbd5d89b39d30522da3f707ae26a1a Mon Sep 17 00:00:00 2001 From: Christophe Pradal Date: Mon, 5 Feb 2024 22:23:12 +0100 Subject: [PATCH 22/22] Update meta.yaml --- conda/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/conda/meta.yaml b/conda/meta.yaml index becdabf..899f9c9 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -9,7 +9,9 @@ build: number: 0 preserve_egg_dir: True string: phenomenal - script: {{PYTHON}} setup.py install + script: + - {{PYTHON}} setup.py build_ext -j{{ CPU_COUNT }} + - {{ PYTHON }} -m pip install . -vv requirements: host: