From 196a2930820534a45192eaa445efdfaba90d9cc2 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Wed, 2 Apr 2025 13:03:06 +0200 Subject: [PATCH 1/5] Sort by workflows --- .github/workflows/aiida.yml | 33 -------------------------- .github/workflows/jobflow.yml | 2 +- .github/workflows/pyiron.yml | 33 -------------------------- .github/workflows/{load.yml => qe.yml} | 9 +++++-- environment.yml | 12 +++------- environment_qe.yml | 10 ++++++++ 6 files changed, 21 insertions(+), 78 deletions(-) delete mode 100644 .github/workflows/aiida.yml delete mode 100644 .github/workflows/pyiron.yml rename .github/workflows/{load.yml => qe.yml} (69%) create mode 100644 environment_qe.yml diff --git a/.github/workflows/aiida.yml b/.github/workflows/aiida.yml deleted file mode 100644 index e269ed6..0000000 --- a/.github/workflows/aiida.yml +++ /dev/null @@ -1,33 +0,0 @@ -name: aiida - -on: - push: - branches: [ main ] - pull_request: - -jobs: - build: - - 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: environment.yml - auto-activate-base: false - - name: Installation and setup - shell: bash -l {0} - run: | - pip install -e qe_xml_parser - pip install -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=$(pwd)/espresso/pseudo - papermill aiida_simple.ipynb aiida_simple_out.ipynb -k "python3" - papermill aiida_qe.ipynb aiida_qe_out.ipynb -k "python3" diff --git a/.github/workflows/jobflow.yml b/.github/workflows/jobflow.yml index bc9a53c..cecf079 100644 --- a/.github/workflows/jobflow.yml +++ b/.github/workflows/jobflow.yml @@ -29,5 +29,5 @@ jobs: shell: bash -l {0} run: | export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo - papermill jobflow_simple.ipynb jobflow_simple_out.ipynb -k "python3" + papermill jobflow_qe.ipynb jobflow_qe_out.ipynb -k "python3" \ No newline at end of file diff --git a/.github/workflows/pyiron.yml b/.github/workflows/pyiron.yml deleted file mode 100644 index 808e152..0000000 --- a/.github/workflows/pyiron.yml +++ /dev/null @@ -1,33 +0,0 @@ -name: pyiron - -on: - push: - branches: [ main ] - pull_request: - -jobs: - build: - - 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: environment.yml - auto-activate-base: false - - name: Installation and setup - shell: bash -l {0} - run: | - pip install -e qe_xml_parser - pip install -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=$(pwd)/espresso/pseudo - papermill pyiron_base_simple.ipynb pyiron_base_simple_out.ipynb -k "python3" - papermill pyiron_base_qe.ipynb pyiron_base_qe_out.ipynb -k "python3" diff --git a/.github/workflows/load.yml b/.github/workflows/qe.yml similarity index 69% rename from .github/workflows/load.yml rename to .github/workflows/qe.yml index ab550cd..4ab4cb2 100644 --- a/.github/workflows/load.yml +++ b/.github/workflows/qe.yml @@ -1,4 +1,4 @@ -name: universal +name: quantum espresso on: push: @@ -12,6 +12,9 @@ jobs: steps: - uses: actions/checkout@v4 + - name: Setup environment + shell: bash -l {0} + run: tail --lines=+4 environment_qe.yml >> environment.yml - uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true @@ -29,5 +32,7 @@ jobs: shell: bash -l {0} run: | export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo - papermill universal_workflow_simple.ipynb universal_workflow_simple_out.ipynb -k "python3" + papermill aiida_qe.ipynb aiida_qe_out.ipynb -k "python3" + papermill jobflow_qe.ipynb jobflow_qe_out.ipynb -k "python3" + papermill pyiron_base_qe.ipynb pyiron_base_qe_out.ipynb -k "python3" papermill universal_workflow_qe.ipynb universal_workflow_qe_out.ipynb -k "python3" diff --git a/environment.yml b/environment.yml index 641ff13..f349295 100644 --- a/environment.yml +++ b/environment.yml @@ -2,13 +2,7 @@ channels: - conda-forge dependencies: - python=3.12 -- pyiron_base=0.11.8 -- qe=7.2 -- qe-tools=2.0.0 -- ase=3.24.0 -- matplotlib=3.10.1 -- xmlschema=3.4.3 -- jobflow=0.1.19 -- pygraphviz=1.14 -- optimade=1.2.3 - aiida-workgraph=0.5.0 +- jobflow=0.1.19 +- pyiron_base=0.11.8 + diff --git a/environment_qe.yml b/environment_qe.yml new file mode 100644 index 0000000..7a2d617 --- /dev/null +++ b/environment_qe.yml @@ -0,0 +1,10 @@ +channels: +- conda-forge +dependencies: +- ase=3.24.0 +- matplotlib=3.10.1 +- xmlschema=3.4.3 +- pygraphviz=1.14 +- optimade=1.2.3 +- qe=7.2 +- qe-tools=2.0.0 \ No newline at end of file From 1f19d69b81d6fc711c5b55b22f020c612ebde67b Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Wed, 2 Apr 2025 13:19:57 +0200 Subject: [PATCH 2/5] fix simple workflow --- .github/workflows/{jobflow.yml => simple.yml} | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) rename .github/workflows/{jobflow.yml => simple.yml} (65%) diff --git a/.github/workflows/jobflow.yml b/.github/workflows/simple.yml similarity index 65% rename from .github/workflows/jobflow.yml rename to .github/workflows/simple.yml index cecf079..884dea9 100644 --- a/.github/workflows/jobflow.yml +++ b/.github/workflows/simple.yml @@ -1,4 +1,4 @@ -name: jobflow +name: simple on: push: @@ -28,6 +28,7 @@ jobs: - name: Tests shell: bash -l {0} run: | - export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo - - papermill jobflow_qe.ipynb jobflow_qe_out.ipynb -k "python3" \ No newline at end of file + papermill aiida_simple.ipynb aiida_simple_out.ipynb -k "python3" + papermill jobflow_simple.ipynb jobflow_simple_out.ipynb -k "python3" + papermill pyiron_base_simple.ipynb pyiron_base_simple_out.ipynb -k "python3" + papermill universal_workflow_simple.ipynb universal_workflow_simple_out.ipynb -k "python3" \ No newline at end of file From 219c911282a42a3f78aa995c6187597013be6340 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Wed, 2 Apr 2025 13:22:29 +0200 Subject: [PATCH 3/5] fix environment --- environment.yml | 1 + environment_qe.yml | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index f349295..bb8b7e5 100644 --- a/environment.yml +++ b/environment.yml @@ -5,4 +5,5 @@ dependencies: - aiida-workgraph=0.5.0 - jobflow=0.1.19 - pyiron_base=0.11.8 +- pygraphviz=1.14 diff --git a/environment_qe.yml b/environment_qe.yml index 7a2d617..c3fcb89 100644 --- a/environment_qe.yml +++ b/environment_qe.yml @@ -4,7 +4,6 @@ dependencies: - ase=3.24.0 - matplotlib=3.10.1 - xmlschema=3.4.3 -- pygraphviz=1.14 - optimade=1.2.3 - qe=7.2 - qe-tools=2.0.0 \ No newline at end of file From 06730e4b79dc05aeb8a65e30870f9a084b6fe0fd Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Wed, 2 Apr 2025 13:23:02 +0200 Subject: [PATCH 4/5] remove quantum espresso parser from simple workflow --- .github/workflows/simple.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/simple.yml b/.github/workflows/simple.yml index 884dea9..027141d 100644 --- a/.github/workflows/simple.yml +++ b/.github/workflows/simple.yml @@ -21,7 +21,6 @@ jobs: - name: Installation and setup shell: bash -l {0} run: | - pip install -e qe_xml_parser pip install -e python_workflow_definition conda install -c conda-forge jupyter papermill verdi presto --profile-name pwd From bf39b6ae37dd2e80dd530e98fee60ad78cb63de0 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Wed, 2 Apr 2025 13:27:09 +0200 Subject: [PATCH 5/5] update readme --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 78e0c1d..77f9726 100644 --- a/README.md +++ b/README.md @@ -70,7 +70,7 @@ The second workflow example is the calculation of an energy volume curve with Qu initial structure is relaxed, afterward it is strained and the total energy is calculated. * [quantum_espresso_workflow.py](quantum_espresso_workflow.py) Python functions * [workflow_qe.json](workflow_qe.json) Workflow definition in the Python Workflow Definition. -* [environment.yml](environment.yml) Conda environment +* [environment_qe.yml](environment_qe.yml) Conda environment | Example | Explanation | |------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------|