diff --git a/.binder/environment.yml b/.binder/environment.yml deleted file mode 100644 index 5580eb1..0000000 --- a/.binder/environment.yml +++ /dev/null @@ -1,31 +0,0 @@ -name: openfe-notebooks -channels: - - conda-forge -dependencies: - - MDAnalysis - - click - - coverage - - ipywidgets - - lomap2 - - lxml - - mdtraj - - nbval - - networkx - - nglview - - notebook - - openff-forcefields - - openmm - - openmmtools>=0.23.0 - - pip - - plugcli - - pymbar - - pytest - - pytest-cov - - pytest-xdist - - pydantic - - python - - rdkit - - typing_extensions - - gufe>=1.7.0 - - openfe>=1.7.0 - - py3dmol diff --git a/.binder/overrides.json b/.binder/overrides.json deleted file mode 100644 index 7748745..0000000 --- a/.binder/overrides.json +++ /dev/null @@ -1,8 +0,0 @@ -{ - "@jupyterlab/docmanager-extension:plugin": { - "defaultViewers": { - "markdown": "Markdown Preview" - } - } -} - diff --git a/.binder/postBuild b/.binder/postBuild deleted file mode 100644 index 3a6057f..0000000 --- a/.binder/postBuild +++ /dev/null @@ -1,5 +0,0 @@ -#!/usr/bin/env bash -set -eux - -mkdir -p ${NB_PYTHON_PREFIX}/share/jupyter/lab/settings -cp .binder/overrides.json ${NB_PYTHON_PREFIX}/share/jupyter/lab/settings diff --git a/.github/workflows/CI.yml b/.github/workflows/ci.yaml similarity index 90% rename from .github/workflows/CI.yml rename to .github/workflows/ci.yaml index 21e2725..0140533 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/ci.yaml @@ -1,4 +1,4 @@ -name: full_tests +name: CI on: push: @@ -33,15 +33,15 @@ jobs: python-version: ["3.12"] steps: - - uses: actions/checkout@v2.4.0 + - uses: actions/checkout@v4 - name: Get current date id: date run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}" - - uses: mamba-org/setup-micromamba@v1 + - uses: mamba-org/setup-micromamba@v2 with: - environment-file: .binder/environment.yml + environment-file: environment.yaml cache-environment: true cache-downloads: true cache-environment-key: environment-${{ steps.date.outputs.date }} diff --git a/.github/workflows/openfe-doc-build.yaml b/.github/workflows/openfe-doc-build.yaml index c77eeef..b372d61 100644 --- a/.github/workflows/openfe-doc-build.yaml +++ b/.github/workflows/openfe-doc-build.yaml @@ -1,4 +1,4 @@ -name: Test openfe doc build +name: Test OpenFE Docs Build on: workflow_dispatch: diff --git a/README.md b/README.md index d9d1d37..63e61da 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,6 @@ [![Logo](https://img.shields.io/badge/OSMF-OpenFreeEnergy-%23002f4a)](https://openfree.energy/) -[![full_tests](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/CI.yml/badge.svg)](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/CI.yml) +[![CI](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/ci.yaml/badge.svg)](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/CI.yml) +[![Docs](https://github.com/OpenFreeEnergy/ExampleNotebooks/actions/workflows/openfe-doc-build.yaml/badge.svg)](https://docs.openfree.energy/en/stable/?badge=stable) [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/OpenFreeEnergy/ExampleNotebooks/master.svg)](https://results.pre-commit.ci/latest/github/OpenFreeEnergy/ExampleNotebooks/main) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/OpenFreeEnergy/ExampleNotebooks/blob/main/showcase/openfe_showcase.ipynb) diff --git a/environment.yaml b/environment.yaml new file mode 100644 index 0000000..c2f6347 --- /dev/null +++ b/environment.yaml @@ -0,0 +1,17 @@ +name: openfe-notebooks +channels: + - conda-forge +dependencies: + - coverage + - ipywidgets + - lxml + - nbval + - nglview + - notebook + - pip + - pytest + - pytest-cov + - pytest-xdist + - python + - gufe >=1.7.0, <1.8.0 + - openfe==1.8.0