Merge pull request #242 from pyiron/pyproject_toml

Switch to pyproject.toml

.ci_support/release.py

@@ -0,0 +1,61 @@
+def get_setup_version_and_pattern(setup_content):
+    depend_lst, version_lst = [], []
+    for l in setup_content:
+        if '==' in l:
+            lst = l.split('[')[-1].split(']')[0].replace(' ', '').replace('"', '').replace("'", '').split(',')
+            for dep in lst:
+                if dep != '\n':
+                    version_lst.append(dep.split('==')[1])
+                    depend_lst.append(dep.split('==')[0])
+
+    version_high_dict = {d: v for d, v in zip(depend_lst, version_lst)}
+    return version_high_dict
+
+
+def get_env_version(env_content):
+    read_flag = False
+    depend_lst, version_lst = [], []
+    for l in env_content:
+        if 'dependencies:' in l:
+            read_flag = True
+        elif read_flag:
+            lst = l.replace('-', '').replace(' ', '').replace('\n', '').split("=")
+            if len(lst) == 2:
+                depend_lst.append(lst[0])
+                version_lst.append(lst[1])
+    return {d:v for d, v in zip(depend_lst, version_lst)}
+
+
+def update_dependencies(setup_content, version_low_dict, version_high_dict):
+    version_combo_dict = {}
+    for dep, ver in version_high_dict.items():
+        if dep in version_low_dict.keys() and version_low_dict[dep] != ver:
+            version_combo_dict[dep] = dep + ">=" + version_low_dict[dep] + ",<=" + ver
+        else:
+            version_combo_dict[dep] = dep + "==" + ver
+
+    setup_content_new = ""
+    pattern_dict = {d:d + "==" + v for d, v in version_high_dict.items()}
+    for l in setup_content:
+        for k, v in pattern_dict.items():
+            if v in l:
+                l = l.replace(v, version_combo_dict[k])
+        setup_content_new +=l
+    return setup_content_new
+
+
+if __name__ == "__main__":
+    with open('pyproject.toml', "r") as f:
+        setup_content = f.readlines()
+
+    with open('environment.yml', "r") as f:
+        env_content = f.readlines()
+
+    setup_content_new = update_dependencies(
+        setup_content=setup_content[2:],
+        version_low_dict=get_env_version(env_content=env_content),
+        version_high_dict=get_setup_version_and_pattern(setup_content=setup_content[2:]),
+    )
+
+    with open('pyproject.toml', "w") as f:
+        f.writelines("".join(setup_content[:2]) + setup_content_new)

.github/workflows/black.yml

@@ -12,7 +12,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: psf/black@stable
       with:
         options: "--check --diff"

.github/workflows/coverage.yml

@@ -16,9 +16,8 @@ env:
 jobs:
   build:
     runs-on: ubuntu-latest
-
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Setup environment
         run: |
           cp .ci_support/environment.yml environment.yml
@@ -31,26 +30,12 @@ jobs:
           channels: conda-forge
           channel-priority: strict
           activate-environment: my-env
+          environment-file: environment.yml
           use-mamba: true
-      - name: Set cache date and number
-        run: |
-          echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV
-          cat .github/variables/cache_number.env >> $GITHUB_ENV
-      - uses: actions/cache@v2
-        with:
-          path: /usr/share/miniconda3/envs/my-env
-          key: coverage-conda-${{ hashFiles('environment.yml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }}
-        id: cache
-      - name: Update environment
-        run: mamba env update -n my-env -f environment.yml
-        if: steps.cache.outputs.cache-hit != 'true'
-      - name: Setup
-        shell: bash -l {0}
-        run: |
-          pip install --no-deps .
       - name: Test
         shell: bash -l {0}
         run: |
+          pip install --no-deps .
           coverage run --omit pysqa/_version.py -m unittest discover tests
           coverage combine
       - name: Coveralls

.github/workflows/dependabot.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     if: (github.actor == 'dependabot[bot]')
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.pull_request.head.ref }} # Check out the head of the actual branch, not the PR
           fetch-depth: 0 # otherwise, you will fail to push refs to dest repo

.github/workflows/deploy.yml

@@ -18,19 +18,17 @@ jobs:
     permissions:
       id-token: write
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v4
       with:
         python-version: "3.11"
-
     - name: Install dependencies
-      run: >-
-        python -m pip install --user --upgrade setuptools wheel
+      run: python -m pip install --user --upgrade setuptools wheel
     - name: Convert dependencies
-      run: >-
-        sed -i 's/==/>=/g' setup.py; cat setup.py
+      run: |
+        cp .ci_support/environment-old.yml environment.yml
+        python .ci_support/release.py; cat pyproject.toml
     - name: Build
-      run: >-
-        python setup.py sdist bdist_wheel
+      run: python setup.py sdist bdist_wheel
     - name: Publish distribution 📦 to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/format_black.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
         ref: ${{ github.event.pull_request.head.ref }} # Check out the head of the actual branch, not the PR
@@ -22,7 +22,7 @@ jobs:
       uses: psf/black@stable
       with:
         options: ""
-        src: "./pysqa"
+        src: ./${{ github.event.repository.name }}
     - name: commit
       run: |
         git config --local user.email "[email protected]"

.github/workflows/mini.yml

@@ -9,16 +9,12 @@ on:
   pull_request:
     branches: [ main ]
 
-env:
-      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
-
 jobs:
   build:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Setup environment
         run: |
           cp .ci_support/environment.yml environment.yml
@@ -33,23 +29,10 @@ jobs:
           channels: conda-forge
           channel-priority: strict
           activate-environment: my-env
+          environment-file: environment.yml
           use-mamba: true
-      - name: Set cache date and number
-        run: |
-          echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV
-          cat .github/variables/cache_number.env >> $GITHUB_ENV
-      - uses: actions/cache@v2
-        with:
-          path: /usr/share/miniconda3/envs/my-env
-          key: mini-conda-${{ hashFiles('environment.yml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }}
-        id: cache
-      - name: Update environment
-        run: mamba env update -n my-env -f environment.yml
-        if: steps.cache.outputs.cache-hit != 'true'
-      - name: Setup
+      - name: Test
         shell: bash -l {0}
         run: |
           pip install --no-deps .
-      - name: Test
-        shell: bash -l {0}
-        run: python -m unittest discover tests
+          python -m unittest discover tests

.github/workflows/pypicheck.yml

@@ -14,30 +14,17 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Setup environment
-        run: cp .ci_support/environment.yml environment.yml
+      - uses: actions/checkout@v4
       - name: Setup Mambaforge
         uses: conda-incubator/setup-miniconda@v2
         with:
-          python-version: '3.10'
+          python-version: '3.11'
           miniforge-variant: Mambaforge
           channels: conda-forge
           channel-priority: strict
           activate-environment: my-env
+          environment-file: .ci_support/environment.yml
           use-mamba: true
-      - name: Set cache date and number
-        run: |
-          echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV
-          cat .github/variables/cache_number.env >> $GITHUB_ENV
-      - uses: actions/cache@v2
-        with:
-          path: /usr/share/miniconda3/envs/my-env
-          key: linux-64-py-3-10-conda-${{ hashFiles('environment.yml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }}
-        id: cache
-      - name: Update environment
-        run: mamba env update -n my-env -f environment.yml
-        if: steps.cache.outputs.cache-hit != 'true'
       - name: Pip check
         shell: bash -l {0}
         run: |

.github/workflows/unittest.yml

@@ -9,13 +9,8 @@ on:
   pull_request:
     branches: [ main ]
 
-env: 
-      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
-
 jobs:
   build:
-
     runs-on: ${{ matrix.operating-system }}
     strategy:
       matrix:
@@ -51,9 +46,7 @@ jobs:
             prefix: /usr/share/miniconda3/envs/my-env
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Setup environment
-        run: cp .ci_support/environment.yml environment.yml
+      - uses: actions/checkout@v4
       - name: Setup Mambaforge
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -62,23 +55,10 @@ jobs:
           channels: conda-forge
           channel-priority: strict
           activate-environment: my-env
+          environment-file: .ci_support/environment.yml
           use-mamba: true
-      - name: Set cache date and number
-        run: |
-          echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV
-          cat .github/variables/cache_number.env >> $GITHUB_ENV
-      - uses: actions/cache@v2
-        with:
-          path: ${{ matrix.prefix }}
-          key: ${{ matrix.label }}-conda-${{ hashFiles('environment.yml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }}
-        id: cache
-      - name: Update environment
-        run: mamba env update -n my-env -f environment.yml
-        if: steps.cache.outputs.cache-hit != 'true'
-      - name: Setup
+      - name: Test
         shell: bash -l {0}
         run: |
           pip install --no-deps .
-      - name: Test
-        shell: bash -l {0}
-        run: python -m unittest discover tests
+          python -m unittest discover tests

.github/workflows/unittests_old.yml

@@ -11,10 +11,9 @@ on:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Setup Mambaforge
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -23,12 +22,10 @@ jobs:
           channels: conda-forge
           channel-priority: strict
           activate-environment: my-env
+          environment-file: .ci_support/environment-old.yml
           use-mamba: true
-      - name: Update environment
-        run: mamba env update -n my-env -f .ci_support/environment-old.yml
-      - name: Setup
-        shell: bash -l {0}
-        run: pip install --no-deps .
       - name: Test
         shell: bash -l {0}
-        run: python -m unittest discover tests
+        run: |
+          pip install --no-deps .
+          python -m unittest discover tests

MANIFEST.in

@@ -1,3 +1 @@
-include LICENSE
-include versioneer.py
-include pysqa/_version.py
+include LICENSE

pyproject.toml

@@ -0,0 +1,65 @@
+[build-system]
+requires = ["jinja2", "pandas", "pyyaml", "setuptools", "versioneer[toml]==0.29"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pysqa"
+description = "Simple HPC queuing system adapter for Python on based jinja templates to automate the submission script creation."
+authors = [
+    { name = "Jan Janssen", email = "[email protected]" },
+]
+readme = "README.md"
+license = { file = "LICENSE" }
+keywords = ["pyiron"]
+requires-python = ">=3.8"
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Topic :: Scientific/Engineering :: Physics",
+    "License :: OSI Approved :: BSD License",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+dependencies = [
+    "jinja2==3.1.2",
+    "pandas==2.1.3",
+    "pyyaml==6.0.1",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/pyiron/pysqa"
+Documentation = "https://pysqa.readthedocs.io"
+Repository = "https://github.com/pyiron/pysqa"
+
+[project.optional-dependencies]
+sge = ["defusedxml==0.7.1"]
+remote = [
+    "paramiko==3.3.1",
+    "tqdm==4.66.1",
+]
+executor = [
+    "pympipool==0.7.5",
+    "cloudpickle==3.0.0",
+]
+
+[project.scripts]
+pysqa = "pysqa.cmd:command_line"
+pysqa-executor = "pysqa.executor.backend:command_line"
+
+[tool.setuptools]
+packages = ["pysqa"]
+
+[tool.setuptools.dynamic]
+version = {attr = "pysqa.__version__"}
+
+[tool.versioneer]
+VCS = "git"
+style = "pep440-pre"
+versionfile_source = "pysqa/_version.py"
+parentdir_prefix = "pysqa"
+tag_prefix = "pysqa-"