Merge pull request #1236 from pyiron/switch_setup

Switch to pyproject.toml

.ci_support/environment-notebooks.yml

@@ -1,5 +1,5 @@
 channels:
-  - conda-forge
+- conda-forge
 dependencies:
-  - jupyter
-  - papermill
+- jupyter
+- papermill

.ci_support/environment-old.yml

@@ -0,0 +1,18 @@
+channels:
+- conda-forge
+dependencies:
+- dill =0.3.1.1
+- gitpython =3.1.23
+- h5io =0.1.2
+- h5py =3.6.0
+- jinja2 =2.11.3
+- numpy =1.23.5
+- pandas =2.0.0
+- pint =0.18
+- psutil =5.8.0
+- pyfileindex =0.0.16
+- pysqa =0.1.5
+- pytables =3.6.1
+- sqlalchemy =2.0.22
+- tqdm =4.66.1
+- traitlets =5.1.1

.ci_support/environment.yml

@@ -1,7 +1,6 @@
 channels:
 - conda-forge
 dependencies:
-- coveralls
 - coverage
 - codacy-coverage
 - dill =0.3.7

.ci_support/pip_install.sh

@@ -0,0 +1,2 @@
+pip install versioneer[toml]==0.29
+pip install . --no-deps --no-build-isolation

.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)

.ci_support/test_backwards.sh

@@ -1,13 +1,14 @@
 #!/bin/bash
 
-pip install --no-deps pyiron_base==0.1.21
+pip install pyiron_base==0.1.21 --no-deps
 echo "Before save";
 for t in tests/backwards/*save.py; do
     echo "Running $t";
     python $t
 done
 
-pip install --no-deps .
+pip install versioneer[toml]==0.29
+pip install . --no-deps --no-build-isolation
 i=0;
 echo "Before loading";
 for t in tests/backwards/*load.py; do

.github/workflows/atomistics-compat.yml

@@ -20,28 +20,28 @@ jobs:
       matrix:
         include:
           - operating-system: macos-latest
-            python-version: '3.10'
+            python-version: '3.11'
             label: osx-64-py-3-10
             prefix: /Users/runner/miniconda3/envs/my-env
 
           - operating-system: windows-latest
-            python-version: '3.10'
+            python-version: '3.11'
             label: win-64-py-3-10
             prefix: C:\Miniconda3\envs\my-env
 
           - operating-system: ubuntu-latest
-            python-version: '3.10'
+            python-version: '3.11'
             label: linux-64-py-3-10
             prefix: /usr/share/miniconda3/envs/my-env
 
     steps:
-    - uses: actions/checkout@v2
-    - name: pyiron_atomistic
+    - uses: actions/checkout@v4
+    - name: Merge environment
       run: |
-        pip install PyYAML
         git clone https://github.com/pyiron/pyiron_atomistics ../pyiron_atomistics
         grep -v "pyiron_base" ../pyiron_atomistics/.ci_support/environment.yml > ../pyiron_atomistics/environment.yml
-        python .ci_support/condamerge.py --base .ci_support/environment.yml --add ../pyiron_atomistics/environment.yml > environment.yml
+        cp .ci_support/environment.yml environment.yml
+        tail --lines=+4 ../pyiron_atomistics/environment.yml >> environment.yml
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v2
       with:
@@ -50,38 +50,17 @@ 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: ${{ 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: pyironconfig
-      shell: bash -l {0}
-      run: |
-        cd ../pyiron_atomistics
-        python .ci_support/pyironconfig.py
-        cd ../pyiron_base
-    - name: Install pyiron_atomistics
+    - name: Tests
       shell: bash -l {0}
+      timeout-minutes: 30
       run: |
+        pip install versioneer[toml]==0.29
         cd ../pyiron_atomistics
-        pip install --no-deps .
+        pip install . --no-deps --no-build-isolation
         cd ../pyiron_base
-    - name: Install pyiron_base
-      shell: bash -l {0}
-      run: |
-        pip install --no-deps .
-    - name: Test
-      shell: bash -l {0}
-      timeout-minutes: 30
-      run: |
+        pip install . --no-deps --no-build-isolation
         cd ../pyiron_atomistics
+        python .ci_support/pyironconfig.py
         python -m unittest discover tests/

.github/workflows/backwards.yml

@@ -10,39 +10,26 @@ on:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
-
     steps:
-    - uses: actions/checkout@v2
-    - name: Setup environment
+    - uses: actions/checkout@v4
+    - name: Merge environment
       run: |
-        python .ci_support/condamerge.py --base .ci_support/environment.yml --add .ci_support/environment-notebooks.yml > environment.yml
+        cp .ci_support/environment.yml environment.yml
+        tail --lines=+4 .ci_support/environment-notebooks.yml >> environment.yml
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v2
       with:
-        python-version: '3.10'
+        python-version: ${{ matrix.python-version }}
         miniforge-variant: Mambaforge
         channels: conda-forge
         channel-priority: strict
         activate-environment: my-env
+        environment-file: environment.yml
         use-mamba: true
-    - name: Set cache date and number
-      run: |
-        echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV
-        cat .github/variables/cache_number.env >> $GITHUB_ENV
-    - uses: actions/cache@v2
-      with:
-        path: /usr/share/miniconda3/envs/my-env
-        key: linux-64-py-3-10-conda-${{ 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: Setup
+    - name: Tests
       shell: bash -l {0}
+      timeout-minutes: 30
       run: |
         python .ci_support/pyironconfig.py
-    - name: Test
-      shell: bash -l {0}
-      run: ./.ci_support/test_backwards.sh
+        ./.ci_support/test_backwards.sh