python-workflow-definition/.github/workflows/pipeline.yml at 4e568afd44032e15b8fba0aed3fce7ac29fadee0 · pythonworkflow/python-workflow-definition · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
name: Pipeline

on:
  push:
    branches: [ main ]
  pull_request:

jobs:
  black:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - uses: psf/black@stable
      with:
        options: "--check --diff"
        src: ./python_workflow_definition/src/python_workflow_definition
    - uses: psf/black@stable
      with:
        options: "--check --diff"
        src: ./example_workflows/quantum_espresso/qe_xml_parser/src/qe_xml_parser

  pip_check:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - name: Setup Mambaforge
      uses: conda-incubator/setup-miniconda@v3
      with:
        auto-update-conda: true
        python-version: "3.12"
        environment-file: binder/environment.yml
        auto-activate-base: false
    - name: Pip check
      shell: bash -l {0}
      run: |
        pip install --no-deps --no-build-isolation -e python_workflow_definition
        pip check

  nfdi4ing:
    runs-on: ubuntu-22.04
    steps:
    - uses: actions/checkout@v4
    - uses: conda-incubator/setup-miniconda@v3
      with:
        auto-update-conda: true
        python-version: "3.12"
        environment-file: binder/environment.yml
        auto-activate-base: false
    - name: Installation and setup
      shell: bash -l {0}
      run: |
        pip install --no-deps --no-build-isolation -e python_workflow_definition
        conda install -c conda-forge jupyter papermill
        verdi presto --profile-name pwd
        sudo apt-get install -y $(cat binder/apt.txt)
    - name: Create Additional Conda Environments
      shell: bash -l {0}
      run: |
        conda env create -n preprocessing -f example_workflows/nfdi/source/envs/preprocessing.yaml -y
        conda env create -n processing -f example_workflows/nfdi/source/envs/processing.yaml -y
        conda env create -n postprocessing -f example_workflows/nfdi/source/envs/postprocessing.yaml -y
    - name: Tests
      shell: bash -l {0}
      run: |
        cd example_workflows/nfdi/
        papermill aiida.ipynb aiida_out.ipynb -k "python3"
        papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
        papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
        papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"

  quantumespresso:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - name: Setup environment
      shell: bash -l {0}
      run: tail --lines=+4 example_workflows/quantum_espresso/environment.yml >> binder/environment.yml
    - uses: conda-incubator/setup-miniconda@v3
      with:
        auto-update-conda: true
        python-version: "3.12"
        environment-file: binder/environment.yml
        auto-activate-base: false
    - name: Installation and setup
      shell: bash -l {0}
      run: |
        pip install --no-deps --no-build-isolation -e example_workflows/quantum_espresso/qe_xml_parser
        pip install --no-deps --no-build-isolation -e python_workflow_definition
        conda install -c conda-forge jupyter papermill
        verdi presto --profile-name pwd
    - name: Tests
      shell: bash -l {0}
      run: |
        export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo
        cp -r example_workflows/quantum_espresso/espresso .
        cd example_workflows/quantum_espresso
        papermill aiida.ipynb aiida_out.ipynb -k "python3"
        papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
        papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
        papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"

  arithmetic:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - uses: conda-incubator/setup-miniconda@v3
      with:
        auto-update-conda: true
        python-version: "3.12"
        environment-file: binder/environment.yml
        auto-activate-base: false
    - name: Installation and setup
      shell: bash -l {0}
      run: |
        pip install --no-deps --no-build-isolation -e python_workflow_definition
        conda install -c conda-forge jupyter papermill
        verdi presto --profile-name pwd
    - name: Tests
      shell: bash -l {0}
      run: |
        cd example_workflows/arithmetic
        papermill aiida.ipynb aiida_out.ipynb -k "python3"
        papermill jobflow.ipynb jobflow_out.ipynb -k "python3"
        papermill pyiron_base.ipynb pyiron_base_out.ipynb -k "python3"
        papermill universal_workflow.ipynb universal_workflow_out.ipynb -k "python3"

  documentation:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          python-version: "3.12"
          environment-file: documentation/environment.yml
          auto-activate-base: false
      - name: Install Jupyterbook
        shell: bash -l {0}
        run: |
          cp documentation/_config.yml .
          cp documentation/_toc.yml .
          cp documentation/*.md .
          jupyter-book build . --path-output public
          mv public/_build/html public_html
          touch public_html/.nojekyll