Merge main

.ci_support/environment-docs.yml

@@ -7,7 +7,7 @@ dependencies:
 - myst-parser
 - aimsgb =1.1.0
 - ase =3.23.0
-- atomistics =0.1.31
+- atomistics =0.1.32
 - defusedxml =0.7.1
 - h5py =3.11.0
 - matplotlib-base =3.9.2
@@ -17,14 +17,14 @@ dependencies:
 - pandas =2.2.2
 - phonopy =2.26.6
 - pint =0.24.3
-- pyiron_base =0.9.12
+- pyiron_base =0.10.1
 - pyiron_snippets =0.1.4
-- pylammpsmpi =0.2.23
+- pylammpsmpi =0.2.25
 - pyscal3 =3.2.7
 - scikit-learn =1.5.1
-- scipy =1.14.0
+- scipy =1.14.1
 - seekpath =2.1.0
 - spglib =2.5.0
-- structuretoolkit =0.0.27
+- structuretoolkit =0.0.28
 - pyxtal =0.6.2
 - jupyter-book =1.0.0

.ci_support/environment-old.yml

@@ -13,7 +13,7 @@ dependencies:
 - pandas =2.0.3
 - phonopy =2.20.0
 - pint =0.18
-- pyiron_base =0.9.12
+- pyiron_base =0.10.0
 - pyiron_snippets =0.1.3
 - pylammpsmpi =0.2.18
 - pyscal3 =3.2.5

.ci_support/environment.yml

@@ -3,7 +3,7 @@ channels:
 dependencies:
 - aimsgb =1.1.0
 - ase =3.23.0
-- atomistics =0.1.31
+- atomistics =0.1.32
 - coverage
 - codacy-coverage
 - defusedxml =0.7.1
@@ -15,13 +15,13 @@ dependencies:
 - pandas =2.2.2
 - phonopy =2.26.6
 - pint =0.24.3
-- pyiron_base =0.9.12
+- pyiron_base =0.10.1
 - pyiron_snippets =0.1.4
-- pylammpsmpi =0.2.23
+- pylammpsmpi =0.2.25
 - pyscal3 =3.2.7
 - scikit-learn =1.5.1
-- scipy =1.14.0
+- scipy =1.14.1
 - seekpath =2.1.0
 - spglib =2.5.0
-- structuretoolkit =0.0.27
+- structuretoolkit =0.0.28
 - pyxtal =0.6.2

.github/workflows/backwards.yml

@@ -18,16 +18,14 @@ jobs:
       run: |
         cp .ci_support/environment.yml environment.yml
         tail --lines=+4 .ci_support/environment-notebooks.yml >> environment.yml
+        echo -e "channels:\n  - conda-forge\n" > .condarc
     - name: Setup Mambaforge
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: '3.10'
-        miniforge-variant: Mambaforge
-        channels: conda-forge
-        channel-priority: strict
-        activate-environment: my-env
+        miniforge-version: latest
+        condarc-file: .condarc
         environment-file: environment.yml
-        use-mamba: true
     - name: Test
       shell: bash -l {0}
       run: |

.github/workflows/benchmarks.yml

@@ -30,16 +30,16 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+      - name: Conda config
+        shell: bash -l {0}
+        run: echo -e "channels:\n  - conda-forge\n" > .condarc
       - name: Setup Mambaforge
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: ${{ matrix.python-version }}
-          miniforge-variant: Mambaforge
-          channels: conda-forge
-          channel-priority: strict
-          activate-environment: my-env
+          miniforge-version: latest
+          condarc-file: .condarc
           environment-file: .ci_support/environment.yml
-          use-mamba: true
       - name: Tests
         shell: bash -l {0}
         timeout-minutes: 30

.github/workflows/deploy.yml

@@ -19,14 +19,13 @@ jobs:
       id-token: write
     steps:
     - uses: actions/checkout@v4
-    - uses: conda-incubator/[email protected]
+    - name: Conda config
+      run: echo -e "channels:\n  - conda-forge\n" > .condarc
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: "3.12"
-        mamba-version: "*"
-        channels: conda-forge
-        miniforge-variant: Mambaforge
-        channel-priority: strict
-        auto-update-conda: true
+        miniforge-version: latest
+        condarc-file: .condarc
         environment-file: .ci_support/environment.yml
     - name: Convert dependencies
       run: |

.github/workflows/integration.yml

@@ -22,16 +22,14 @@ jobs:
         run: |
           cp .ci_support/environment.yml environment.yml
           tail --lines=+4 .ci_support/environment-notebooks.yml >> environment.yml
+          echo -e "channels:\n  - conda-forge\n" > .condarc
       - name: Setup Mambaforge
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: '3.12'
-          miniforge-variant: Mambaforge
-          channels: conda-forge
-          channel-priority: strict
-          activate-environment: my-env
+          miniforge-version: latest
+          condarc-file: .condarc
           environment-file: environment.yml
-          use-mamba: true
       - name: Test
         shell: bash -l {0}
         run: |

.github/workflows/integration_unittests.yml

@@ -22,16 +22,14 @@ jobs:
       run: |
         cp .ci_support/environment.yml environment.yml
         tail --lines=+4 .ci_support/environment-notebooks.yml >> environment.yml
+        echo -e "channels:\n  - conda-forge\n" > .condarc
     - name: Setup Mambaforge
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: '3.12'
-        miniforge-variant: Mambaforge
-        channels: conda-forge
-        channel-priority: strict
-        activate-environment: my-env
+        miniforge-version: latest
+        condarc-file: .condarc
         environment-file: environment.yml
-        use-mamba: true
     - name: Tests
       shell: bash -l {0}
       run: |

.github/workflows/notebooks.yml

@@ -13,21 +13,19 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Merge environment
         run: |
           cp .ci_support/environment.yml environment.yml
           tail --lines=+4 .ci_support/environment-notebooks.yml >> environment.yml
+          echo -e "channels:\n  - conda-forge\n" > .condarc
       - name: Setup Mambaforge
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: '3.12'
-          miniforge-variant: Mambaforge
-          channels: conda-forge
-          channel-priority: strict
-          activate-environment: my-env
+          miniforge-version: latest
+          condarc-file: .condarc
           environment-file: environment.yml
-          use-mamba: true
       - name: Test
         shell: bash -l {0}
         run: |

.github/workflows/pypicheck.yml

@@ -12,16 +12,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
+    - name: Conda config
+      run: echo -e "channels:\n  - conda-forge\n" > .condarc
     - name: Setup Mambaforge
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: '3.12'
-        miniforge-variant: Mambaforge
-        channels: conda-forge
-        channel-priority: strict
-        activate-environment: my-env
+        miniforge-version: latest
+        condarc-file: .condarc
         environment-file: .ci_support/environment.yml
-        use-mamba: true
     - name: Pip check
       shell: bash -l {0}
       run: |

.github/workflows/unittests.yml

@@ -40,16 +40,16 @@ jobs:
 
     steps:
       - uses: actions/checkout@v2
+      - name: Conda config
+        shell: bash -l {0}
+        run: echo -e "channels:\n  - conda-forge\n" > .condarc
       - name: Setup Mambaforge
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: ${{ matrix.python-version }}
-          miniforge-variant: Mambaforge
-          channels: conda-forge
-          channel-priority: strict
-          activate-environment: my-env
+          miniforge-version: latest
+          condarc-file: .condarc
           environment-file: .ci_support/environment.yml
-          use-mamba: true
       - name: Test
         shell: bash -l {0}
         timeout-minutes: 30

.github/workflows/unittests_old.yml

@@ -10,16 +10,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
+    - name: Conda config
+      run: echo -e "channels:\n  - conda-forge\n" > .condarc
     - name: Setup Mambaforge
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
-        python-version: '3.9'
-        miniforge-variant: Mambaforge
-        channels: conda-forge
-        channel-priority: strict
-        activate-environment: my-env
+        python-version: '3.10'
+        miniforge-version: latest
+        condarc-file: .condarc
         environment-file: .ci_support/environment-old.yml
-        use-mamba: true
     - name: Test
       shell: bash -l {0}
       timeout-minutes: 30

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.1
+    rev: v0.6.3
     hooks:
       - id: ruff
         name: ruff lint

binder/environment.yml

@@ -3,7 +3,7 @@ channels:
 dependencies:
 - aimsgb =1.1.0
 - ase =3.23.0
-- atomistics =0.1.31
+- atomistics =0.1.32
 - defusedxml =0.7.1
 - h5py =3.11.0
 - matplotlib-base =3.9.2
@@ -13,15 +13,15 @@ dependencies:
 - pandas =2.2.2
 - phonopy =2.26.6
 - pint =0.24.3
-- pyiron_base =0.9.12
+- pyiron_base =0.10.1
 - pyiron_snippets =0.1.4
-- pylammpsmpi =0.2.23
+- pylammpsmpi =0.2.25
 - pyscal3 =3.2.7
 - scikit-learn =1.5.1
-- scipy =1.14.0
+- scipy =1.14.1
 - seekpath =2.1.0
 - spglib =2.5.0
-- structuretoolkit =0.0.27
+- structuretoolkit =0.0.28
 - pyxtal =0.6.2
 - pyiron-data =0.0.30
 - sqsgenerator =0.3

pyiron_atomistics/atomistics/job/atomistic.py

@@ -297,9 +297,9 @@ def calc_md(
             self._generic_input["time_step"] = int(time_step)
         self._generic_input.remove_keys(["max_iter"])
 
-    def from_dict(self, job_dict):
-        super().from_dict(job_dict=job_dict)
-        self._generic_input.from_dict(obj_dict=job_dict["input"]["generic"])
+    def from_dict(self, obj_dict):
+        super().from_dict(obj_dict=obj_dict)
+        self._generic_input.from_dict(obj_dict=obj_dict["input"]["generic"])
 
     def to_dict(self):
         job_dict = super(AtomisticGenericJob, self).to_dict()
@@ -818,14 +818,12 @@ def _structure_to_dict(self):
         else:
             return None
 
-    def _structure_from_dict(self, job_dict):
+    def _structure_from_dict(self, obj_dict):
         if (
-            "structure" in job_dict["input"].keys()
+            "structure" in obj_dict["input"].keys()
             and self._generic_input["structure"] == "atoms"
         ):
-            self.structure = Atoms().from_dict(
-                atoms_dict=job_dict["input"]["structure"]
-            )
+            self.structure = Atoms().from_dict(obj_dict=obj_dict["input"]["structure"])
 
     def _structure_to_hdf(self):
         data_dict = self._structure_to_dict()
@@ -840,7 +838,7 @@ def _structure_from_hdf(self):
         ):
             with self.project_hdf5.open("input/structure") as hdf5_input:
                 self.structure = Atoms().from_dict(
-                    hdf5_input.read_dict_from_hdf(recursive=True)
+                    obj_dict=hdf5_input.read_dict_from_hdf(recursive=True)
                 )
 
     def _write_chemical_formular_to_database(self):

pyiron_atomistics/atomistics/master/quasi.py

@@ -271,6 +271,6 @@ def plot_free_energy_volume_temperature(
         )
         scalarmappaple = matplotlib.cm.ScalarMappable(norm=normalize, cmap=cmap)
         scalarmappaple.set_array(temperatures)
-        cbar = matplotlib.pyplot.colorbar(scalarmappaple)
+        cbar = matplotlib.pyplot.colorbar(scalarmappaple, ax=axis)
         cbar.set_label("Temperature")
         return axis