Build: Update dependencies (#227)

* Update full dependencies
* Update core dependencies
* Fix repr test for newer python version

* Update Python version in actions
* Allow recent poetry version in actions
* Install current version of mdtraj

* Update Readme

Author: martin-schlipf

.github/workflows/install.yml

@@ -22,7 +22,7 @@ jobs:
       uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
-        python-version: 3.9
+        python-version: "3.10"
     - name: Install py4vasp and testing tools
       shell: bash -el {0}
       run: |

.github/workflows/test_core.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v4
@@ -24,7 +24,7 @@ jobs:
       run: |
         python --version
         python -m pip install --progress-bar=off --upgrade pip
-        pip install --progress-bar=off "poetry!=1.4.1"
+        pip install --progress-bar=off poetry
     - name: Install py4vasp-core
       run: |
         cp core/* .

.github/workflows/test_full.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v4
@@ -26,7 +26,7 @@ jobs:
       run: |
         python --version
         python -m pip install --progress-bar=off --upgrade pip
-        pip install --progress-bar=off "poetry<2"
+        pip install --progress-bar=off poetry
     - name: Install py4vasp
       shell: bash -el {0}
       run: |
@@ -36,7 +36,7 @@ jobs:
       shell: bash -el {0}
       run: |
         conda info
-        conda install -q -c conda-forge "mdtraj<1.10.2"
+        conda install -q -c conda-forge mdtraj
     - name: Test with pytest
       shell: bash -el {0}
       run: |

README.md

@@ -18,10 +18,10 @@ We recommend installing py4vasp in a conda environment to resolve issues related
 installing `mdtraj` with pip. To do this please use the following steps. The last step
 will test whether everything worked
 ~~~shell
-conda create --name py4vasp-env python=3.9
+conda create --name py4vasp-env python=3.10
 git clone git@github.com:vasp-dev/py4vasp.git
 conda activate py4vasp-env
-pip install "poetry<2"
+pip install poetry
 cd py4vasp
 poetry install
 conda install -c conda-forge mdtraj

core/poetry.lock

@@ -28,17 +28,19 @@ repository = "https://github.com/vasp-dev/py4vasp"
 
 
 [tool.poetry.dependencies]
-python = ">=3.9"
-numpy = ">=1.23"
-h5py = ">=3.7.0"
+python = ">=3.10"
+numpy = ">=2.0"
+h5py = ">=3.9.0"
 
 [tool.poetry.group.dev.dependencies]
-pytest = ">=7.1.2"
-pytest-cov = ">=3.0.0"
-pylint = ">=2.15"
-hypothesis = ">=6.48.1"
-black = ">=22.6.0"
-isort = ">=5.10.1"
+pytest = ">=8.0"
+pytest-cov = ">=5.0"
+pylint = ">=3.0"
+hypothesis = ">=6.79"
+black = ">=23.7"
+isort = ">=5.13"
+ipykernel = ">=6.25.0"
+pre-commit = ">=3.3.3"
 
 [tool.isort]
 profile = "black"

core/pyproject.toml

@@ -15,7 +15,7 @@ authors = [
     "Andreas Singraber <andreas.singraber@vasp.at>",
     "Alexey Tal <alexey.tal@vasp.at>",
     "Tomáš Bučko <tomas.bucko@uniba.sk>",
-    "Max Liebetreu <max.liebetreu@vasp.at>"
+    "Max Liebetreu <max.liebetreu@vasp.at>",
 ]
 license = "Apache-2.0"
 readme = "README.md"
@@ -27,31 +27,31 @@ repository = "https://github.com/vasp-dev/py4vasp"
 
 
 [tool.poetry.dependencies]
-python = ">=3.9"
-numpy = ">=1.23"
-h5py = ">=3.7.0"
-pandas = ">=1.4.3"
+python = ">=3.10"
+numpy = ">=2.0"
+h5py = ">=3.9.0"
+pandas = ">=2.0"
 nglview = ">=3.0.5"
-ase = ">=3.22.1"
-plotly = ">=5.9.0"
-kaleido = ">=0.2.1,<0.2.1.post1 || >0.2.1.post1"
-ipython = ">=8.12"
+ase = ">=3.23"
+plotly = ">=5.23"
+kaleido = ">=1.0"
+ipython = ">=8.26"
 scipy = ">=1.12.0"
 click = ">=8.1.8"
 
 [tool.poetry.group.dev.dependencies]
-pytest = ">=7.1.2"
-pytest-cov = ">=3.0.0"
-pylint = ">=2.15"
-hypothesis = ">=6.48.1"
-black = ">=22.6.0"
-isort = ">=5.10.1"
+pytest = ">=8.0"
+pytest-cov = ">=5.0"
+pylint = ">=3.0"
+hypothesis = ">=6.79"
+black = ">=23.7"
+isort = ">=5.13"
 ipykernel = ">=6.25.0"
 pre-commit = ">=3.3.3"
 
 [tool.poetry.group.doc.dependencies]
-sphinx = ">=5.0.2"
-sphinx-automodapi = ">=0.14.1"
+sphinx = ">=8.0"
+sphinx-automodapi = ">=0.16"
 
 [tool.poetry.scripts]
 py4vasp = "py4vasp.cli:cli"

poetry.lock

@@ -21,6 +21,10 @@ def test_repr():
 def check_repr_is_consistent(instance, quantity):
     class_name = convert.to_camelcase(quantity)
     module = importlib.import_module(f"py4vasp._calculation.{quantity}")
-    locals()[class_name] = getattr(module, class_name)
-    copy = eval(repr(instance))
+    eval_globals = {
+        class_name: getattr(module, class_name),
+        "PosixPath": PosixPath,
+        "WindowsPath": WindowsPath,
+    }
+    copy = eval(repr(instance), eval_globals)
     assert copy.__class__ == instance.__class__