diff --git a/.github/workflows/test_notebooks.yml b/.github/workflows/test_notebooks.yml index fae6100..4a81184 100644 --- a/.github/workflows/test_notebooks.yml +++ b/.github/workflows/test_notebooks.yml @@ -3,3 +3,31 @@ name: Test notebooks +on: + push: + branches: [ master ] + pull_request: + branches: [ master ] + schedule: + # daily at 06:15 + - cron: 15 06 * * * + + +jobs: + test: + runs-on: ubuntu-latest + name: test + steps: + - uses: actions/checkout@v2 + + - name: install mamba + uses: mamba-org/provision-with-micromamba@main + with: + environment-file: environment-test.yml + environment-name: foyer-tutorials + + # linux and osx + - name: run nbval + shell: bash -l {0} + run: | + python -m pytest --nbval-lax --sanitize-with nbval_sanitize.cfg --verbose diff --git a/Foyer_00_Getting_Started.ipynb b/Foyer_00_Getting_Started.ipynb index 58e9fd0..28c4f9c 100644 --- a/Foyer_00_Getting_Started.ipynb +++ b/Foyer_00_Getting_Started.ipynb @@ -108,7 +108,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.5.5" + "version": "3.8.10" } }, "nbformat": 4, diff --git a/Foyer_01_SMARTS_and_Overrides.ipynb b/Foyer_01_SMARTS_and_Overrides.ipynb index 135e705..3185ea2 100644 --- a/Foyer_01_SMARTS_and_Overrides.ipynb +++ b/Foyer_01_SMARTS_and_Overrides.ipynb @@ -109,7 +109,6 @@ "source": [ "import mbuild as mb\n", "\n", - "hexane = mb.recipes.Alkane(6)\n", "\n", "hexane.save('hexane.top', forcefield_files='utils/OPLSaa_alkanes.xml', overwrite=True)\n", @@ -185,7 +184,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.8" + "version": "3.8.10" } }, "nbformat": 4, diff --git a/Foyer_02_SMARTS_for_Non-Atomistic_Systems.ipynb b/Foyer_02_SMARTS_for_Non-Atomistic_Systems.ipynb index 2780c94..0549374 100644 --- a/Foyer_02_SMARTS_for_Non-Atomistic_Systems.ipynb +++ b/Foyer_02_SMARTS_for_Non-Atomistic_Systems.ipynb @@ -234,7 +234,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.8" + "version": "3.8.10" } }, "nbformat": 4, diff --git a/Foyer_03_Creating_Force_field_Files.ipynb b/Foyer_03_Creating_Force_field_Files.ipynb index e4087eb..42ff0ac 100644 --- a/Foyer_03_Creating_Force_field_Files.ipynb +++ b/Foyer_03_Creating_Force_field_Files.ipynb @@ -86,7 +86,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.8" + "version": "3.8.10" } }, "nbformat": 4, diff --git a/environment-test.yml b/environment-test.yml new file mode 100644 index 0000000..01c1d87 --- /dev/null +++ b/environment-test.yml @@ -0,0 +1,25 @@ +name: foyer-tutorials + +channels: + - conda-forge + +dependencies: + - python>=3.6 + - numpy + - scipy + - packmol>=20 + - nglview>=3 + - parmed + - mdtraj + - gsd + - py3Dmol + - jupyter + - nbformat + - ipython=7.10.0 + - networkx + - requests + - lxml + - foyer + - mbuild + - pytest + - nbval diff --git a/environment.yml b/environment.yml index caaf289..8d9e0e0 100644 --- a/environment.yml +++ b/environment.yml @@ -1,30 +1,23 @@ -name: mbuild-binder +name: foyer-binder channels: - conda-forge - - defaults - - mosdef - - omnia - - glotzer - - bioconda dependencies: - - python=3.5 + - python>=3.6 - numpy - scipy - - packmol=1.0.0 - - nglview>=0.6.2.3 - - oset + - packmol>=20 + - nglview>=3 - parmed - mdtraj - gsd - - openbabel + - py3Dmol - jupyter - nbformat - - ipykernel - - openmm + - ipython=7.10.0 - networkx - - six - - plyplus - requests - lxml + - foyer + - mbuild diff --git a/nbval_sanitize.cfg b/nbval_sanitize.cfg new file mode 100644 index 0000000..d079c0f --- /dev/null +++ b/nbval_sanitize.cfg @@ -0,0 +1,7 @@ +[regex1] +regex: \d{1,2}/\d{1,2}/\d{2,4} +replace: DATE-STAMP + +[regex2] +regex: \d{2}:\d{2}:\d{2} +replace: TIME-STAMP