Merge pull request #1 from Fluorescence-Tools/development

Development

.github/workflows/conda-build.yml

@@ -0,0 +1,59 @@
+name: Conda Build
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - development
+  release:
+    types: ['released', 'prereleased']
+  schedule:
+    # Every Monday at 11PM UTC
+    - cron: "0 11 * * 1"
+
+jobs:
+  build-linux:
+    name: CondaBuild (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.10"]
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+
+      - name: "Set SDK on MacOS (if needed)"
+        if: startsWith(matrix.os, 'macos')
+        run: tools/install_macos_sdk.sh
+
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          channel-priority: true
+
+      - name: Display Conda Settings
+        shell: bash -el {0}
+        run: |
+          conda info
+          conda list
+          conda config --show-sources
+          conda config --show
+          printenv | sort
+
+      - name: Build Conda Package
+        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

@@ -0,0 +1,56 @@
+
+name: Build and Upload Conda Packages
+
+on:
+  workflow_dispatch:
+  release:
+    types: ['released', 'prereleased']
+  schedule:
+    # At 11:00 AM, every 3 months
+    - cron: "0 11 * */3 *"
+
+jobs:
+  build:
+    name: CondaBuild (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.10"]
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+
+      - name: "Set SDK on MacOS (if needed)"
+        if: startsWith(matrix.os, 'macos')
+        run: tools/install_macos_sdk.sh
+
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          channel-priority: true
+
+      - name: Display Conda Settings
+        shell: bash -el {0}
+        run: |
+          conda info
+          conda list
+          conda config --show-sources
+          conda config --show
+          printenv | sort
+
+      - name: Build and Upload Conda Package
+        uses: aganders3/headless-gui@v1
+        with:
+          shell: bash -el {0}
+          run: |
+            mamba install conda-build boa anaconda-client
+            cd conda-recipe
+            curl -sLO https://github.com/conda-forge/conda-forge-pinning-feedstock/raw/main/recipe/conda_build_config.yaml
+            conda mambabuild . --output-folder conda-bld -c tpeulen
+            anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u tpeulen --force conda-bld/**/*.tar.bz2

.github/workflows/gitlab-sync.yml

@@ -0,0 +1,22 @@
+name: GitlabSync
+
+on:
+  workflow_dispatch:
+  push:
+
+jobs:
+  sync:
+    runs-on: ubuntu-latest
+    name: Git Repo Sync
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - uses: wangchucheng/[email protected]
+        with:
+          # Such as https://github.com/wangchucheng/git-repo-sync.git
+          target-url: ${{ secrets.TARGET_URL }}
+          # Such as wangchucheng
+          target-username: ${{ secrets.TARGET_USERNAME }}
+          # You can store token in your project's 'Setting > Secrets' and reference the name here. Such as ${{ secrets.ACCESS\_TOKEN }}
+          target-token: ${{ secrets.TARGET_TOKEN }}

.gitlab-ci.yml

@@ -1,50 +1,92 @@
-{% set data = load_setup_py_data(setup_file='../setup.py', from_recipe_dir=True) %}
+stages:
+  - build
+  - test
+  - deploy
 
-package:
-  name: {{ data.get('name')|lower }}
-  version: {{ data.get('version')|lower }}
+build:linux:
+  stage: build
+  tags:
+    - linux
+  image: condaforge/mambaforge:latest
+  before_script:
+    - apt update -yq && apt -yq install build-essential
+    - git submodule update --init --recursive --remote
+    - cd tools && git pull --force && cd ..
+  script:
+    - ./tools/build.sh
+  artifacts:
+    paths:
+      - bld-dir/
 
-source:
-  path: ..
+build:windows:
+  image: mambaforge:vs16
+  tags:
+    - win
+  stage: build
+  before_script:
+    - cd tools && git pull --force && cd ..
+    - git submodule update --init --recursive --remote
+  script:
+    - cmd.exe
+    - conda activate base
+    - git submodule update --init --recursive --remote
+    - .\tools\build.bat
+  artifacts:
+    paths:
+      - bld-dir/
 
-build:
-  number: 0
-  string: py{{ python }}
-  entry_points:
-    {% for entry_point_type, entry_points in data.get("entry_points", dict()).items() -%}
-    {% for entry_point in entry_points -%}
-    - {{ entry_point }}
-    {% endfor %}
-    {% endfor %}
-requirements:
-  host:
-    - python
-    - numpy
-    - pyyaml
-    - setuptools
-  build:
-    - python
-    - numpy
-    - setuptools
-    - pyyaml
-  run:
-    - python
-    - numpy
-    - pyyaml
-    - qtpy
-    - pyqt
-    - pyqtgraph
-    - tttrlib
-    - pathlib2  # [py < 3]
+build:osx:
+  stage: build
+  tags:
+    - osx
+  before_script:
+    - cd tools && git pull --force && cd ..
+    - git submodule update --init --recursive --remote
+  script:
+    - ./tools/build.sh
+  artifacts:
+    paths:
+      - bld-dir/
 
-about:
-  home: {{ data.get('url') }}
-  license: {{ data.get('license') }}
-  license_file: LICENSE
-  summary: Converter for TTTR files
-  description: |
-    {{ data.get('description') }}
+test:linux:
+  stage: test
+  tags:
+    - linux
+  image:
+    name: condaforge/mambaforge
+  before_script:
+    # Issue with OpenGL and X11 display
+    # See: https://stackoverflow.com/questions/65675765/is-it-possible-to-run-x11-on-gitlab-ci
+    # See: https://github.com/conda-forge/pygridgen-feedstock/issues/10
+    # procps is used to grep the process by name to kill it when needed
+    - apt update -yq
+    - apt install -yq xorg-dev libglu1-mesa libgl1-mesa-dev xvfb libxinerama1 libxcursor1 libgl1-mesa-glx procps
+  script:
+    - source activate
+    # Disable Numba JIT for correct coverage analysis
+    - export NUMBA_DISABLE_JIT=1
+    - cp tools/.condarc ~/.condarc
+    - conda config --add channels "file://`pwd`/bld-dir"
+    - mamba create -n test python tttrconvert
+    - conda activate test
+    # Run GUI with xvfb - no X11 screen
+    - |
+      xvfb-run -a -s "-screen 0 1400x900x24 +extension RANDR" -- tttrconvert &
+      sleep 10
+      pgrep -f tttrconvert | awk '{print "kill -9 " $1}' | sh
 
-extra:
-  recipe-maintainers:
-    - tpeulen
+deploy:conda:
+  tags:
+    - linux
+  image: condaforge/mambaforge:latest
+  stage: deploy
+  dependencies:
+    - build:linux
+    - build:windows
+    - build:osx
+  script:
+    - ./tools/deploy.sh
+
+#chisurf:
+#  stage: Trigger-cross-projects
+#  trigger: chisurf/chisurf

README.md

@@ -1,9 +1,12 @@
 # tttrconvert
 
-A ``tttrconvert`` is a tool to convert time-tagged time-resolved files into different formats. ``tttrconvert`` to read 
+A ``tttrconvert`` is a very basic tool to convert time-tagged time-resolved files into different formats. ``tttrconvert`` to read 
 and write TTTR files ``tttrconvert`` uses ``tttrlib``. The tool ``tttrconvert`` can be embedded 
 in other software and is part of ChiSurf.
 
+Currently, the tool has only very basic functions (it is probably not
+what you want).
+
 ![tttrconvert GUI][1]
 
 ## Building and installation
@@ -15,7 +18,7 @@ To install ``tttrconvert`` from the source code clone the git repository and run
 setup script.
 
 ```commandline
-git clone https://gitlab.peulen.xyz/tpeulen/tttrconvert
+git clone https://github.com/fluorescence-tools/tttrconvert
 cd tttrconvert
 python setup.py install
 ```
@@ -26,23 +29,17 @@ tttrconvert
 ```
 
 ### Conda
-``tttrconvert`` depends on common python packages such as ``numpy``. Additionally, ``tttrconvert`` depends on 
-``tttrlib``. Thus, to install ``k2dist`` make sure that conda channels that provide packages for the necessary
-dependencies are listed in the ``.condarc`` file 
-
-```yaml
-channels:
-  - tpeulen
-  - tpeulen/label/nightly
-  - conda-forge
-  - defaults
-```
+`tttrconvert` can be installed using conda, best in a separate
+environment
 
-To avoid potential conflicts ``tttrconvert`` can be installed in a separate environment. 
+```bash
+conda create tttrconvert
+mamba install tttrconvert -c tpeulen
+```
 
-```commandline
-conda create -n test
-conda install tttrconvert
+To us the tool activate the tttrconvert environment and start the tool
+from the command line.
+```bash
 conda activate tttrconvert
 tttrconvert
 ```
@@ -51,11 +48,7 @@ tttrconvert
 
 ## Graphical user interface
 First, select the input file type. Next, add files to the file list by drag-and-drop. Finally,
-select the ouput file format and save/convert the files.
-
-## Note on meta-data
-The different TTTR file formats contain and support different meta-data. The meta-data may need to be 
-edited separately.
+select the output file format and save/convert the files.
 
 
 [1]: doc/gui.png "tttrconvert GUI"