Merge pull request #47 from Fluorescence-Tools/development

Development

.github/workflows/conda-build.yml

@@ -5,6 +5,9 @@ on:
   push:
     branches:
       - development
+  schedule:
+    # Every Monday at 11PM UTC
+    - cron: "0 11 * * 1"
 
 jobs:
   build-linux:
@@ -19,6 +22,10 @@ jobs:
       - name: Checkout Repository
         uses: actions/checkout@v2
 
+      - name: "Set SDK on MacOS (if needed)"
+        if: startsWith(matrix.os, 'macos')
+        run: build_tools/install_macos_sdk.sh
+
       - name: Set up Conda
         uses: conda-incubator/setup-miniconda@v3
         with:
@@ -38,11 +45,14 @@ jobs:
           printenv | sort
 
       - name: Build Conda Package
-        shell: bash -el {0}
-        run: |
-          conda config --add channels tpeulen
-          mamba install conda-build boa
-          cd conda-recipe
-          curl -sLO  https://raw.githubusercontent.com/conda-forge/conda-forge-pinning-feedstock/084b098a28a7a66e9a0967d156bc55b9ebfc6726/recipe/conda_build_config.yaml
-          # curl -sLO https://github.com/conda-forge/conda-forge-pinning-feedstock/raw/main/recipe/conda_build_config.yaml
-          conda mambabuild .
+        uses: aganders3/headless-gui@v1
+        with:
+          shell: bash -el {0}
+          run: |
+            conda config --add channels tpeulen
+            mamba install conda-build boa
+            cd conda-recipe
+            # curl -sLO  https://raw.githubusercontent.com/conda-forge/conda-forge-pinning-feedstock/084b098a28a7a66e9a0967d156bc55b9ebfc6726/recipe/conda_build_config.yaml
+            # curl -sLO https://github.com/conda-forge/conda-forge-pinning-feedstock/raw/main/recipe/conda_build_config.yaml
+            conda mambabuild .
+  

.github/workflows/conda-release.yml

@@ -22,6 +22,10 @@ jobs:
       - name: Checkout Repository
         uses: actions/checkout@v2
 
+      - name: "Set SDK on MacOS (if needed)"
+        if: startsWith(matrix.os, 'macos')
+        run: build_tools/install_macos_sdk.sh
+
       - name: Set up Conda
         uses: conda-incubator/setup-miniconda@v3
         with:
@@ -41,15 +45,17 @@ jobs:
           printenv | sort
 
       - name: Build Conda Package
-        shell: bash -el {0}
-        run: |
-          mamba install conda-build boa anaconda-client
-          conda config --add channels tpeulen
-          cd conda-recipe
-          # Use older conda_build_config -> boost-cpp 1.78
-          curl -sLO  https://raw.githubusercontent.com/conda-forge/conda-forge-pinning-feedstock/084b098a28a7a66e9a0967d156bc55b9ebfc6726/recipe/conda_build_config.yaml
-          # curl -sLO https://github.com/conda-forge/conda-forge-pinning-feedstock/raw/main/recipe/conda_build_config.yaml
-          conda mambabuild . --output-folder ../conda-bld
+        uses: aganders3/headless-gui@v1
+        with:
+          shell: bash -el {0}
+          run: |
+            mamba install conda-build boa anaconda-client
+            conda config --add channels tpeulen
+            cd conda-recipe
+            # Use older conda_build_config -> boost-cpp 1.78
+            # curl -sLO  https://raw.githubusercontent.com/conda-forge/conda-forge-pinning-feedstock/084b098a28a7a66e9a0967d156bc55b9ebfc6726/recipe/conda_build_config.yaml
+            # curl -sLO https://github.com/conda-forge/conda-forge-pinning-feedstock/raw/main/recipe/conda_build_config.yaml
+            conda mambabuild . --output-folder ../conda-bld
 
       - name: Upload Conda Package
         shell: bash -el {0}

.prospector.yml

@@ -9,7 +9,7 @@ pep8:
     disable:
       - N803 # argument name should be lowercase
       - N806 # variable in function should be lowercase
-      - N812 # lowercase imported as non lowercase
+      - N812 # lowercase imported as non-lowercase
 
 pylint:
     run: true

README.md

@@ -1,7 +1,4 @@
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/814238f7b1a14f87821beadabc758408)](https://www.codacy.com/manual/tpeulen/ChiSurf?utm_source=github.com&utm_medium=referral&utm_content=Fluorescence-Tools/ChiSurf&utm_campaign=Badge_Grade)
-[![Codacy Badge](https://api.codacy.com/project/badge/Coverage/814238f7b1a14f87821beadabc758408)](https://www.codacy.com/manual/tpeulen/ChiSurf?utm_source=github.com&utm_medium=referral&utm_content=Fluorescence-Tools/ChiSurf&utm_campaign=Badge_Coverage)
-[![Build Status](https://travis-ci.org/Fluorescence-Tools/ChiSurf.svg?branch=master)](https://travis-ci.org/Fluorescence-Tools/ChiSurf)
-[![Build status](https://ci.appveyor.com/api/projects/status/so2ndl1otr8ishjk?svg=true)](https://ci.appveyor.com/project/tpeulen/chisurf)
+![conda build](https://github.com/fluorescence-tools/chisurf/actions/workflows/conda-build.yml/badge.svg)
 [![Anaconda-Server Version](https://anaconda.org/tpeulen/chisurf/badges/version.svg)](https://anaconda.org/tpeulen/chisurf)
 [![DOI](https://zenodo.org/badge/149296509.svg)](https://zenodo.org/badge/latestdoi/149296509)
 

build_tools/install_macos_sdk.sh

@@ -0,0 +1,33 @@
+# See: https://github.com/openmm/openmm/blob/master/devtools/ci/gh-actions/scripts/install_macos_sdk.sh
+
+# Install an older MacOS SDK
+# This should guarantee OpenMM builds with extended compatibility across MacOS versions
+# Adapted from conda-forge-ci-setup scripts:
+# * https://github.com/conda-forge/conda-forge-ci-setup-feedstock/blob/dde296e/recipe/run_conda_forge_build_setup_osx
+# * https://github.com/conda-forge/conda-forge-ci-setup-feedstock/blob/dde296e/recipe/download_osx_sdk.sh
+#
+# Some possible updates might involve upgrading the download link to future MacOS releases (10.15 to something else),
+# depending on the version provided by the CI
+
+OSX_SDK_DIR="$(xcode-select -p)/Platforms/MacOSX.platform/Developer/SDKs"
+export MACOSX_DEPLOYMENT_TARGET=10.9
+export MACOSX_SDK_VERSION=10.9
+
+export CMAKE_OSX_SYSROOT="${OSX_SDK_DIR}/MacOSX${MACOSX_SDK_VERSION}.sdk"
+
+if [[ ! -d ${CMAKE_OSX_SYSROOT}} ]]; then
+    echo "Downloading ${MACOSX_SDK_VERSION} sdk"
+    curl -L -O --connect-timeout 5 --max-time 10 --retry 5  --retry-delay 0 --retry-max-time 40 --retry-connrefused --retry-all-errors \
+        https://github.com/phracker/MacOSX-SDKs/releases/download/10.15/MacOSX${MACOSX_SDK_VERSION}.sdk.tar.xz
+    tar -xf MacOSX${MACOSX_SDK_VERSION}.sdk.tar.xz -C "$(dirname ${CMAKE_OSX_SYSROOT})"
+fi
+
+if [[ "$MACOSX_DEPLOYMENT_TARGET" == 10.* ]]; then
+# set minimum sdk version to our target
+plutil -replace MinimumSDKVersion -string ${MACOSX_SDK_VERSION} $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist
+plutil -replace DTSDKName -string macosx${MACOSX_SDK_VERSION}internal $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist
+fi
+
+echo "MACOSX_DEPLOYMENT_TARGET=${MACOSX_DEPLOYMENT_TARGET}" >> ${GITHUB_ENV}
+echo "CMAKE_OSX_SYSROOT=${MACOSX_DEPLOYMENT_TARGET}" >> ${GITHUB_ENV}
+echo "CMAKE_OSX_SYSROOT=${CMAKE_OSX_SYSROOT}" >> ${GITHUB_ENV}

conda-recipe/conda_build_config.yaml

@@ -1,5 +1,5 @@
-CONDA_BUILD_SYSROOT:
-  - /opt/MacOSX10.13.sdk        # [osx]
+#CONDA_BUILD_SYSROOT:
+#  - /opt/MacOSX10.9.sdk        # [osx]
 c_compiler:
   - gcc                        # [linux]
   - clang                      # [osx]

conda-recipe/meta.yaml

@@ -52,6 +52,7 @@ requirements:
     - matplotlib
     - deprecation
     - scikit-fluorescence
+    - imp
     - typing_extensions 4.5.*
     - typing_utils 0.1.*
     - scipy 1.11.*
@@ -67,6 +68,8 @@ requirements:
     - pytools 2023.*
     - emcee 3.1.*
     - pyopengl 3.1.*
+    - pocl  >=0.14      # [linux or osx]
+    - oclgrind          # [win]
     - pymol-open-source 2.5.*
     - tttrconvert
     - qscintilla2
@@ -76,6 +79,16 @@ requirements:
     - ndxplorer
     - clsmview
 
+app:
+  entry: chisurf
+  summary: ChiSurf analysis platform for fluorescence data
+
+test:
+  imports:
+    - chisurf
+  commands:
+    - chisurf &        # [linux or osx]
+
 about:
   home: https://github.com/Fluorescence-Tools/ChiSurf
   license: {{ data.get('license') }}