Merge branch 'main' into rm

.ci_support/environment-docs.yml

@@ -2,18 +2,24 @@ channels:
 - conda-forge
 dependencies:
 - nbsphinx
-- dill
-- gitpython
-- h5io
-- h5py
-- jinja2
+- sphinx
+- sphinx_rtd_theme
+- myst-parser
 - numpy
-- pandas
-- pint
-- psutil
-- pyfileindex
-- pysqa
-- pytables
-- sqlalchemy
-- tqdm
-- traitlets
+- cloudpickle =3.0.0
+- gitpython =3.1.42
+- h5io_browser =0.0.9
+- h5py =3.10.0
+- jinja2 =3.1.3
+- monty =2024.2.2
+- numpy =1.26.4
+- pandas =2.2.0
+- pint =0.23
+- psutil =5.9.8
+- pyfileindex =0.0.22
+- pympipool =0.7.13
+- pysqa =0.1.15
+- pytables =3.9.2
+- sqlalchemy =2.0.27
+- tqdm =4.66.2
+- traitlets =5.14.1

.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 +1,20 @@
+channels:
+- conda-forge
+dependencies:
+- cloudpickle =2.0.0
+- gitpython =3.1.23
+- h5io_browser =0.0.6
+- h5py =3.6.0
+- jinja2 =2.11.3
+- monty =2021.3.3
+- numpy =1.23.5
+- pandas =2.0.0
+- pint =0.18
+- psutil =5.8.0
+- pyfileindex =0.0.16
+- pympipool =0.7.11
+- pysqa =0.1.12
+- pytables =3.6.1
+- sqlalchemy =2.0.22
+- tqdm =4.44.0
+- traitlets =5.1.1

.ci_support/environment.yml

@@ -1,21 +1,24 @@
 channels:
 - conda-forge
 dependencies:
-- coveralls
 - coverage
 - codacy-coverage
-- dill =0.3.7
-- gitpython =3.1.37
-- h5io =0.1.9
+- conda =23.11.0
+- conda_subprocess =0.0.1
+- cloudpickle =3.0.0
+- gitpython =3.1.42
+- h5io_browser =0.0.9
 - h5py =3.10.0
-- jinja2 =3.1.2
-- numpy =1.26.0
-- pandas =2.1.1
-- pint =0.22
-- psutil =5.9.5
-- pyfileindex =0.0.12
-- pysqa =0.1.3
-- pytables =3.9.1
-- sqlalchemy =2.0.22
-- tqdm =4.66.1
-- traitlets =5.11.2
+- jinja2 =3.1.3
+- monty =2024.2.2
+- numpy =1.26.4
+- pandas =2.2.0
+- pint =0.23
+- psutil =5.9.8
+- pyfileindex =0.0.22
+- pympipool =0.7.13
+- pysqa =0.1.15
+- pytables =3.9.2
+- sqlalchemy =2.0.27
+- tqdm =4.66.2
+- traitlets =5.14.1

.ci_support/pip_install.sh

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

.ci_support/pypi_vs_conda_names.json

@@ -1,10 +1,4 @@
 {
   "tables": "pytables",
-  "pyiron-base": "pyiron_base",
-  "pyiron-atomistics": "pyiron_atomistics",
-  "pyiron-contrib": "pyiron_contrib",
-  "pyiron-experimental": "pyiron_experimental",
-  "pyiron-continuum": "pyiron_continuum",
-  "pyiron-gpl": "pyiron_gpl",
-  "pyiron-gui": "pyiron_gui"
-}
+  "blosc2": "python-blosc2"
+}

.ci_support/release.py

@@ -0,0 +1,79 @@
+import json
+
+
+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
+
+
+def convert_key(key, convert_dict):
+    if key not in convert_dict.keys():
+        return key
+    else:
+        return convert_dict[key]
+
+
+if __name__ == "__main__":
+    with open('.ci_support/pypi_vs_conda_names.json', 'r') as f:
+        name_conversion_dict = {v: k for k, v in json.load(f).items()}
+
+    with open('pyproject.toml', "r") as f:
+        setup_content = f.readlines()
+
+    with open('environment.yml', "r") as f:
+        env_content = f.readlines()
+
+    env_version_dict = {
+        convert_key(key=k, convert_dict=name_conversion_dict): v 
+        for k, v in get_env_version(env_content=env_content).items()
+    }
+
+    setup_content_new = update_dependencies(
+        setup_content=setup_content[2:],
+        version_low_dict=env_version_dict,
+        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 +50,15 @@ 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
-      shell: bash -l {0}
-      run: |
-        cd ../pyiron_atomistics
-        pip install --no-deps .
-        cd ../pyiron_base
-    - name: Install pyiron_base
-      shell: bash -l {0}
-      run: |
-        pip install --no-deps .
-    - name: Test
+    - name: Tests
       shell: bash -l {0}
       timeout-minutes: 30
       run: |
+        pip install versioneer[toml]==0.29
+        pip install . --no-deps --no-build-isolation
         cd ../pyiron_atomistics
+        pip install . --no-deps --no-build-isolation
+        python .ci_support/pyironconfig.py
         python -m unittest discover tests/