Merge branch 'main' into cp2k

# Conflicts:
#	.ci_support/environment.yml
#	pyiron_contrib/__init__.py
#	setup.py

.ci_support/environment.yml

@@ -5,15 +5,15 @@ dependencies:
 - coveralls
 - coverage
 - codacy-coverage
-- matplotlib =3.5.1
-- numpy =1.22.2
-- pyiron_base =0.5.5
-- pyiron_atomistics =0.2.37
-- pyparsing =3.0.7
-- scipy =1.8.0
-- seaborn =0.11.2
-- scikit-image =0.19.2
+- matplotlib =3.6.1
+- numpy =1.23.4
+- pyiron_base =0.5.26
+- pyiron_atomistics =0.2.58
+- pyparsing =3.0.9
+- scipy =1.9.3
+- seaborn =0.12.0
+- scikit-image =0.19.3
 - randspg =0.0.1
+- boto3 =1.24.96
+- moto =4.0.8
 - pycp2k =0.2.2
-- boto3 =1.21.3
-- moto =3.0.4

.github/delete-merged-branch-config.yml

@@ -1,3 +1,3 @@
 exclude: 
-  - master
+  - main
 delete_closed_pr: false

.github/workflows/UpdateDependabotPR.yml

@@ -2,7 +2,7 @@ name: UpdateDependabotPR
 
 on:
   pull_request_target:
-    branches: [ master ]
+    branches: [ main ]
 
 jobs:
   build:

.github/workflows/coverage.yml

@@ -5,9 +5,9 @@ name: Coverage
 
 on:
   push:
-    branches: [ master ]
+    branches: [ main ]
   pull_request:
-    branches: [ master ]
+    branches: [ main ]
 
 jobs:
   build:

.github/workflows/docs.yml

@@ -0,0 +1,37 @@
+# This workflow is used to test, if the documentation can build
+
+name: Docs
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        python-version: "3.10"
+        mamba-version: "*"
+        channels: conda-forge
+        channel-priority: strict
+        auto-update-conda: true  
+        environment-file: .ci_support/environment.yml
+    - name: Setup
+      shell: bash -l {0}
+      run: |
+        python .ci_support/pyironconfig.py
+        pip install --no-deps .
+        conda env update --name test --file docs/environment.yml
+    - name: Documentation
+      shell: bash -l {0}
+      run: |
+        mkdir public_html; cd docs
+        sphinx-build -b html ./ ../public_html || exit 1;
+        cd ..

.github/workflows/notebooks.yml

@@ -2,30 +2,20 @@ name: Notebooks
 
 on:
   push:
-    branches: [ master ]
+    branches: [ main ]
   pull_request:
-    branches: [ master ]
+    branches: [ main ]
 
 jobs:
-  build:
-
+  build-notebooks:
+    needs: commit-updated-env
     runs-on: ubuntu-latest
-
     steps:
-    - uses: actions/checkout@v2
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        python-version: "3.10"
-        mamba-version: "*"
-        channels: conda-forge
-        channel-priority: strict
-        auto-update-conda: true  
-        environment-file: .ci_support/environment.yml
-    - name: Setup
-      shell: bash -l {0}
-      run: |
-        pip install --no-deps .
-        conda install papermill
-    - name: Tests
-      shell: bash -l {0}
-      run: ./.ci_support/build_notebooks.sh
+      - uses: actions/checkout@v3
+      - uses: pyiron/actions/build-notebooks@main
+        with:
+          python-version: '3.10'
+          env-prefix: /usr/share/miniconda3/envs/my-env
+          env-label: linux-64-py-3-10
+          env-files: .ci_support/environment.yml
+          exclusion-file: .ci_support/exclude

.github/workflows/pypicheck.yml

@@ -2,9 +2,9 @@ name: Pip check
 
 on:
   push:
-    branches: [ master ]
+    branches: [ main ]
   pull_request:
-    branches: [ master ]
+    branches: [ main ]
 
 jobs:
   build:

.github/workflows/unittests.yml

@@ -1,35 +1,43 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Python package
-
+name: Unit Tests
 on:
   push:
-    branches: [ master ]
+    branches: [ main ]
   pull_request:
-    branches: [ master ]
+    branches: [ main ]
 
 jobs:
   build:
-    env:
-      CONDA_PREFIX: /usr/share/miniconda/
 
     runs-on: ${{ matrix.operating-system }}
     strategy:
       matrix:
-        operating-system: [ubuntu-latest]
-        python-version: ["3.8", "3.9", "3.10"]
+        include:
+          - operating-system: ubuntu-latest
+            python-version: '3.10'
+            label: linux-64-py-3-10
+            prefix: /usr/share/miniconda3/envs/my-env
+
+          - operating-system: ubuntu-latest
+            python-version: 3.9
+            label: linux-64-py-3-9
+            prefix: /usr/share/miniconda3/envs/my-env
+
+          - operating-system: ubuntu-latest
+            python-version: 3.8
+            label: linux-64-py-3-8
+            prefix: /usr/share/miniconda3/envs/my-env
 
     steps:
     - uses: actions/checkout@v2
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: pyiron/actions/cached-mamba@main
       with:
         python-version: ${{ matrix.python-version }}
-        mamba-version: "*"
-        channels: conda-forge
-        channel-priority: strict
-        auto-update-conda: true  
-        environment-file: .ci_support/environment.yml
+        env-prefix: ${{ matrix.prefix }}
+        env-label: ${{ matrix.label }}
+        env-files: .ci_support/environment.yml
     - name: Setup
       shell: bash -l {0}
       run: |

.readthedocs.yml

@@ -5,20 +5,21 @@
 # Required
 version: 2
 
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "mambaforge-4.10"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
 
-# Optionally build your docs in additional formats such as PDF and ePub
-formats: []
-
 # Install pyiron from conda 
 conda:
   environment: docs/environment.yml
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
   install:
     - method: pip
       path: .

pyiron_contrib/RDM/storagejob.py

@@ -3,7 +3,7 @@
 import shutil
 
 from pyiron_base import GenericJob, DataContainer
-from pyiron_base.generic.filedata import FileData
+from pyiron_base import FileData
 from pyiron_contrib.generic.s3io import FileS3IO
 
 

pyiron_contrib/__init__.py

@@ -44,6 +44,8 @@
 JOB_CLASS_DICT['Atomicrex'] = 'pyiron_contrib.atomistics.atomicrex.atomicrex_job'
 JOB_CLASS_DICT['StructureMasterInt'] = 'pyiron_contrib.atomistics.atomistics.job.structurelistmasterinteractive'
 JOB_CLASS_DICT['StorageJob'] = 'pyiron_contrib.RDM.storagejob'
+JOB_CLASS_DICT['PacemakerJob'] = 'pyiron_contrib.atomistics.pacemaker.job'
+JOB_CLASS_DICT['MeamFit'] = 'pyiron_contrib.atomistics.meamfit.meamfit'
 JOB_CLASS_DICT['Cp2kJob'] = 'pyiron_contrib.atomistics.cp2k.job'
 
 

pyiron_contrib/atomistics/atomicrex/base.py

@@ -4,8 +4,9 @@
 
 """Pyiron interface to atomicrex"""
 import numpy as np
+import pandas as pd
 
-from pyiron_base import state, GenericJob, Executable
+from pyiron_base import state, GenericJob, Executable, FlattenedStorage
 
 from pyiron_contrib.atomistics.atomicrex.general_input import (
     GeneralARInput,
@@ -15,16 +16,14 @@
 from pyiron_contrib.atomistics.atomicrex.potential_factory import ARPotFactory
 from pyiron_contrib.atomistics.atomicrex.output import Output
 from pyiron_contrib.atomistics.atomicrex.function_factory import FunctionFactory
+from pyiron_contrib.atomistics.ml.potentialfit import PotentialFit
+from pyiron_contrib.atomistics.atomistics.job.trainingcontainer import (
+    TrainingContainer,
+    TrainingStorage,
+)
 
 
-## Class defined for future addition of other codes
-## Not sure which functionality (if any) can be extracted yet, but a similar pattern is followed in other pyiron modules
-class PotentialFittingBase(GenericJob):
-    def __init__(self, project, job_name):
-        super().__init__(project, job_name)
-
-
-class AtomicrexBase(PotentialFittingBase):
+class AtomicrexBase(GenericJob, PotentialFit):
     __version__ = "0.1.0"
     __hdf_version__ = "0.1.0"
     """Class to set up and run atomicrex jobs"""
@@ -217,7 +216,7 @@ def write_input(self, directory=None):
         """
         if directory is None:
             directory = self.working_directory
-        self.input._write_xml_file(directory=directory)
+        self.input._write_xml_file(directory=directory, job=self)
         self.potential.write_xml_file(directory=directory)
         self.structures.write_xml_file(directory=directory)
 
@@ -248,8 +247,7 @@ def _executable_activate(self, enforce=False):
     # instead of the potential_as_pd_df function
     @property
     def lammps_potential(self):
-        pot = self.potential_as_pd_df()
-        return pot
+        return self.potential_as_pd_df()
 
     def potential_as_pd_df(self):
         """
@@ -258,6 +256,26 @@ def potential_as_pd_df(self):
         """
         return self.potential._potential_as_pd_df(job=self)
 
+    #### PotentialFit methods
+    def _add_training_data(self, container: TrainingContainer) -> None:
+        self.structures.add_training_data(container)
+
+    def _get_training_data(self) -> TrainingStorage:
+        return self.structures.get_training_data()
+
+    def _get_predicted_data(self) -> FlattenedStorage:
+        return self.structures.get_predicted_data()
+
+    def get_lammps_potential(self) -> pd.DataFrame:
+        """
+        Return a pyiron compatible dataframe that defines a potential to be used with a Lammps job (or subclass
+        thereof).
+
+        Returns:
+            DataFrame: contains potential information to be used with a Lammps job.
+        """
+        return self.potential_as_pd_df()
+
 
 class Factories:
     """

pyiron_contrib/atomistics/atomicrex/fit_properties.py

@@ -240,7 +240,7 @@ def __init__(self, num_chunks=1, num_elements=1, **kwargs):
         super().__init__(num_chunks=num_chunks, num_elements=num_elements, **kwargs)
         self._per_chunk_arrays = {}
         self.add_array("fit", dtype=bool, per="chunk", fill=False)
-        self.add_array("relative_weight", per="chunk", fill=np.nan)
+        self.add_array("relative_weight", per="chunk", fill=1.0)
         self.add_array("relax", dtype=bool, per="chunk")
         self.add_array("residual_style", per="chunk", dtype=np.ubyte, fill=0)
         self.add_array("output", dtype=bool, per="chunk", fill=False)