Merge pull request #75 from bayer-science-for-a-better-life/ci-switch…

…-to-pip

Ci switch to pip

.github/workflows/run_pytests.yaml

@@ -2,6 +2,9 @@ name: paquo ci
 
 on: [push, pull_request]
 
+env:
+  QUPATH_VERSION: 0.3.2
+
 jobs:
   # RUN PYTEST ON PAQUO SOURCE
   tests:
@@ -22,39 +25,32 @@ jobs:
           - os: ubuntu-latest
             python-version: 3.7
     steps:
-    - uses: actions/checkout@v1
-    - name: Make python reference python3 because conda-devenv needs it
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+    - name: Setup Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
       with:
-        python-version: '3.x'
-    - name: Create the environment.yml via conda-devenv
+        python-version: ${{ matrix.python-version }}
+    - name: Install paquo
       run: |
         python -m pip install --upgrade pip
-        python -m pip install --upgrade setuptools
-        python -m pip install git+https://github.com/ESSS/conda-devenv.git@2.1.1
-        python -m conda_devenv.devenv --env PAQUO_DEVEL=TRUE --file environment.devenv.yml --print > environment.yml
-    - name: Cache conda
-      uses: actions/cache@v1
+        pip install -e .[dev]
+    - name: Restore qupath cache
+      uses: actions/cache@v2
       env:
-        # Increase this value to reset cache if etc/example-environment.yml has not changed
         CACHE_NUMBER: 1
       with:
-        path: ~/conda_pkgs_dir
-        key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
-    - name: Setup conda
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        environment-file: environment.yml
-        python-version: ${{ matrix.python-version }}
-        auto-update-conda: true
-        activate-environment: paquo
-        use-only-tar-bz2: true
-        auto-activate-base: false
-    - shell: bash -l {0}
-      name: Test with pytest
+        path: ./qupath/download
+        key: ${{ runner.os }}-qupath-v${{ env.CACHE_NUMBER }}
+    - name: Install qupath and set PAQUO_QUPATH_DIR
+      shell: bash
+      run: |
+        python -c "import os; os.makedirs('qupath/download', exist_ok=True)"
+        python -c "import os; os.makedirs('qupath/apps', exist_ok=True)"
+        python -m paquo get_qupath --install-path ./qupath/apps --download-path ./qupath/download ${{ env.QUPATH_VERSION }} | grep -v "^#" | sed "s/^/PAQUO_QUPATH_DIR=/" >> $GITHUB_ENV
+    - name: Test with pytest
       run: |
-        conda info
-        conda list
         pytest --cov=./paquo --cov-report=xml
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1
@@ -66,15 +62,16 @@ jobs:
     name: mypy type analysis
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - name: Set up Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install --upgrade setuptools
           pip install -e .[dev]
       - name: Run mypy
         run: |
@@ -87,9 +84,11 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'push' && github.ref == 'refs/heads/main'
     steps:
-      - uses: actions/checkout@v1
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Set up Python
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
       - name: Install dependencies
@@ -132,9 +131,11 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     steps:
-      - uses: actions/checkout@v1
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v1
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Set up Python
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
       - name: Install dependencies

CODEOWNERS

@@ -0,0 +1,2 @@
+# pado code owners
+* @ap--

CONTRIBUTING.md

@@ -0,0 +1,141 @@
+# Contribution Guidelines
+
+
+## Pull requests are always welcome
+
+We're trying very hard to keep our systems simple, lean and focused. We don't
+want them to be everything for everybody. This means that we might decide
+against incorporating a new request.
+
+
+## Create issues...
+
+Any significant change should be documented as a GitHub issue before anybody
+starts working on it.
+
+### ...but check for existing issues first!
+
+Please take a moment to check that an issue doesn't already exist documenting
+your request. If it does, it never hurts to add a quick "+1" or
+"I need this too". This will help prioritize the most common requests.
+
+
+## Conventions
+
+Fork the repository and make changes on your fork on a branch:
+
+1. Create the right type of issue (defect, enhancement, test, etc)
+2. Name the branch N-something where N is the number of the issue.
+
+Note that the maintainers work on branches in this repository.
+
+Work hard to ensure your pull request is valid. This includes code quality,
+clear naming, and including unit tests. Please read the Code Of Conduct at the
+bottom of this file.
+
+Pull request descriptions should be as clear as possible and include a reference
+to all the issues that they address. In GitHub, you can reference an issue by
+adding a line to your commit description that follows the format:
+
+  `Fixes #N`
+
+where N is the issue number.
+
+
+## Merge approval
+
+Repository maintainers will review the pull request and make sure it provides
+the appropriate level of code quality & correctness. 
+
+
+## How are decisions made?
+
+Short answer: with pull requests to this repository.
+
+All decisions, big and small, follow the same 3 steps:
+
+1. Open a pull request. Anyone can do this.
+2. Discuss the pull request. Anyone can do this.
+3. Accept or refuse a pull request. The relevant maintainers do this (see below
+   "Who decides what?")
+
+   1. Accepting pull requests
+      1. If the pull request appears to be ready to merge, approve it.
+
+      2. If the pull request has some small problems that need to be changed,
+         make a comment addressing the issues.
+
+      3. If the changes needed to a PR are small, you can add a "LGTM once the
+         following comments are addressed..." this will reduce needless back and
+         forth.
+
+      4. If the PR only needs a few changes before being merged, any MAINTAINER
+         can make a replacement PR that incorporates the existing commits and
+         fixes the problems before a fast track merge.
+
+   2. Closing pull requests
+      1. If a PR appears to be abandoned, after having attempted to contact the
+         original contributor, then a replacement PR may be made. Once the
+         replacement PR is made, any contributor may close the original one.
+
+      2. If you are not sure if the pull request implements a good feature or
+         you do not understand the purpose of the PR, ask the contributor to
+         provide more documentation. If the contributor is not able to
+         adequately explain the purpose of the PR, the PR may be closed by any
+         MAINTAINER.
+
+      3. If a MAINTAINER feels that the pull request is sufficiently
+         architecturally flawed, or if the pull request needs significantly more
+         design discussion before being considered, the MAINTAINER should close
+         the pull request with a short explanation of what discussion still
+         needs to be had. It is important not to leave such pull requests open,
+         as this will waste both the MAINTAINER's time and the contributor's
+         time. It is not good to string a contributor on for weeks or months,
+         having them make many changes to a PR that will eventually be rejected.
+
+
+## Who decides what?
+
+All decisions are pull requests, and the relevant maintainers make decisions by
+accepting or refusing pull requests. Review and acceptance by anyone is denoted
+by adding a comment in the pull request: `LGTM`. However, only currently listed
+`MAINTAINERS` are counted towards the required majority.
+
+The maintainers will be listed in the MAINTAINER file, all these people will be
+in the employment of Bayer.
+
+
+## I'm a maintainer, should I make pull requests too?
+
+Yes. Nobody should ever push to main directly. All changes should be made
+through a pull request.
+
+## Code Of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all people
+who contribute through reporting issues, posting feature requests, updating
+documentation, submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free
+experience for everyone, regardless of level of experience, gender, gender
+identity and expression, sexual orientation, disability, personal appearance,
+body size, race, ethnicity, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual
+language or imagery, derogatory comments or personal attacks, trolling, public
+or private harassment, insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct. Project maintainers who do not follow the
+Code of Conduct may be removed from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by opening an issue or contacting one or more of the project
+maintainers.
+
+This Code of Conduct is adapted from the Contributor Covenant, version 1.0.0,
+available at
+[https://www.contributor-covenant.org/version/1/0/0/code-of-conduct.html][v1]
+
+[v1]: https://www.contributor-covenant.org/version/1/0/0/code-of-conduct.html

pyproject.toml

@@ -1,8 +1,8 @@
 [build-system]
 requires = [
-  "setuptools >= 42",
+  "setuptools >= 64",
   "wheel",
-  "setuptools_scm[toml]>=3.4",
+  "setuptools_scm[toml]>=6.2",
 ]
 build-backend = "setuptools.build_meta"