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Switch to pixi and rattler build.
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‎.github/workflows/devel.yaml‎

Lines changed: 33 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@ name: Release Devel
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on:
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workflow_dispatch:
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push:
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branches: [ devel ]
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branches: [devel]
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jobs:
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build:
@@ -18,11 +18,9 @@ jobs:
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- { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
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- { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
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exclude:
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# Exclude all but the latest Python from all
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# but Linux
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- platform:
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{ name: "macos", os: "macos-latest", shell: "bash -l {0}" }
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python-version: "3.12" # MacOS can't run 3.12 yet... We want 3.10 and 3.11
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python-version: "3.12" # MacOS can't run 3.12 yet... We want 3.10 and 3.11
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environment:
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name: ghostly-build
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defaults:
@@ -32,30 +30,38 @@ jobs:
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SIRE_DONT_PHONEHOME: 1
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SIRE_SILENT_PHONEHOME: 1
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steps:
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- uses: conda-incubator/setup-miniconda@v3
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#
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- uses: actions/checkout@v4
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with:
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auto-update-conda: true
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python-version: ${{ matrix.python-version }}
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activate-environment: ghostly_build
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miniforge-version: latest
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#
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- name: Clone the devel branch
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run: git clone -b devel https://github.com/openbiosim/ghostly
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#
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- name: Setup Conda
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run: conda install -y -c conda-forge boa anaconda-client packaging
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#
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- name: Update Conda recipe
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run: python ${{ github.workspace }}/ghostly/actions/update_recipe.py
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#
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- name: Prepare build location
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run: mkdir ${{ github.workspace }}/build
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#
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- name: Build Conda package using conda build
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run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/ghostly/recipes/ghostly
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#
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- name: Upload Conda package
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run: python ${{ github.workspace }}/ghostly/actions/upload_package.py
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fetch-depth: 0
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#
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- name: Compute version info
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run: python ${{ github.workspace }}/actions/update_recipe.py
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#
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- name: Create sdist
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run: pip install build && python -m build --sdist && mv dist/*.tar.gz ghostly-source.tar.gz
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working-directory: ${{ github.workspace }}
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#
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- name: Install rattler-build
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uses: prefix-dev/rattler-build-action@v0.2.34
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with:
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tool-version: latest
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build-args: --help
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#
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- name: Write Python variant config
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shell: bash
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run: printf 'python:\n - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
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#
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- name: Build package using rattler-build
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shell: bash
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run: rattler-build build --recipe "${{ github.workspace }}/recipes/ghostly" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"
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#
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- name: Install anaconda-client
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run: python -m pip install anaconda-client
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if: ${{ matrix.platform.name == 'linux' && matrix.python-version == '3.11' }}
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#
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- name: Upload package
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run: python ${{ github.workspace }}/actions/upload_package.py
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env:
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ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
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ANACONDA_LABEL: dev

‎.github/workflows/main.yaml‎

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Original file line numberDiff line numberDiff line change
@@ -23,7 +23,7 @@ jobs:
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exclude:
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- platform:
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{ name: "macos", os: "macos-latest", shell: "bash -l {0}" }
26-
python-version: "3.12" # MacOS can't run 3.12 yet...
26+
python-version: "3.12" # MacOS can't run 3.12 yet...
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environment:
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name: ghostly-build
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defaults:
@@ -33,30 +33,39 @@ jobs:
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SIRE_DONT_PHONEHOME: 1
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SIRE_SILENT_PHONEHOME: 1
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steps:
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- uses: conda-incubator/setup-miniconda@v3
36+
#
37+
- uses: actions/checkout@v4
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with:
38-
auto-update-conda: true
39-
python-version: ${{ matrix.python-version }}
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activate-environment: ghostly_build
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miniforge-version: latest
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#
43-
- name: Clone the main branch
44-
run: git clone -b main https://github.com/openbiosim/ghostly
45-
#
46-
- name: Setup Conda
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run: conda install -y -c conda-forge boa anaconda-client packaging
48-
#
49-
- name: Update Conda recipe
50-
run: python ${{ github.workspace }}/ghostly/actions/update_recipe.py
51-
#
52-
- name: Prepare build location
53-
run: mkdir ${{ github.workspace }}/build
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#
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- name: Build Conda package using conda build
56-
run: conda build -c conda-forge -c openbiosim/label/main ${{ github.workspace }}/ghostly/recipes/ghostly
57-
#
58-
- name: Upload Conda package
59-
run: python ${{ github.workspace }}/ghostly/actions/upload_package.py
39+
ref: main
40+
fetch-depth: 0
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#
42+
- name: Compute version info
43+
run: python ${{ github.workspace }}/actions/update_recipe.py
44+
#
45+
- name: Create sdist
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run: pip install build && python -m build --sdist && mv dist/*.tar.gz ghostly-source.tar.gz
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working-directory: ${{ github.workspace }}
48+
#
49+
- name: Install rattler-build
50+
uses: prefix-dev/rattler-build-action@v0.2.34
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with:
52+
tool-version: latest
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build-args: --help
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#
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- name: Write Python variant config
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shell: bash
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run: printf 'python:\n - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
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#
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- name: Build package using rattler-build
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shell: bash
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run: rattler-build build --recipe "${{ github.workspace }}/recipes/ghostly" -c conda-forge -c openbiosim/label/main --variant-config "${{ github.workspace }}/python_variant.yaml"
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#
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- name: Install anaconda-client
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run: python -m pip install anaconda-client
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if: github.event.inputs.upload_packages == 'true' && matrix.platform.name == 'linux' && matrix.python-version == '3.11'
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#
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- name: Upload package
68+
run: python ${{ github.workspace }}/actions/upload_package.py
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env:
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ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
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ANACONDA_LABEL: main

‎.github/workflows/pr.yaml‎

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@@ -17,14 +17,12 @@ jobs:
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- { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
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- { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
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exclude:
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# Exclude all but the latest Python from all
21-
# but Linux
2220
- platform:
2321
{ name: "macos", os: "macos-latest", shell: "bash -l {0}" }
2422
python-version: "3.10"
2523
- platform:
2624
{ name: "macos", os: "macos-latest", shell: "bash -l {0}" }
27-
python-version: "3.12" # MacOS can't run 3.12 yet...
25+
python-version: "3.12" # MacOS can't run 3.12 yet...
2826
environment:
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name: ghostly-build
3028
defaults:
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SIRE_SILENT_PHONEHOME: 1
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REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}"
3735
steps:
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- uses: conda-incubator/setup-miniconda@v3
36+
#
37+
- uses: actions/checkout@v4
3938
with:
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auto-update-conda: true
41-
python-version: ${{ matrix.python-version }}
42-
activate-environment: ghostly_build
43-
miniforge-version: latest
44-
#
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- name: Clone the feature branch
46-
run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} ghostly
47-
#
48-
- name: Setup Conda
49-
run: conda install -y -c conda-forge boa anaconda-client packaging
50-
#
51-
- name: Update Conda recipe
52-
run: python ${{ github.workspace }}/ghostly/actions/update_recipe.py
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#
54-
- name: Prepare build location
55-
run: mkdir ${{ github.workspace }}/build
56-
#
57-
- name: Build Conda package using conda build using main channel
39+
fetch-depth: 0
40+
#
41+
- name: Compute version info
42+
run: python ${{ github.workspace }}/actions/update_recipe.py
43+
#
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- name: Create sdist
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run: pip install build && python -m build --sdist && mv dist/*.tar.gz ghostly-source.tar.gz
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working-directory: ${{ github.workspace }}
47+
#
48+
- name: Install rattler-build
49+
uses: prefix-dev/rattler-build-action@v0.2.34
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with:
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tool-version: latest
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build-args: --help
53+
#
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- name: Write Python variant config
55+
shell: bash
56+
run: printf 'python:\n - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
57+
#
58+
- name: Build package using rattler-build (main channel)
5859
if: ${{ github.base_ref == 'main' }}
59-
run: conda build -c conda-forge -c openbiosim/label/main ${{ github.workspace }}/ghostly/recipes/ghostly
60-
#
61-
- name: Build Conda package using conda build using dev channel
60+
shell: bash
61+
run: rattler-build build --recipe "${{ github.workspace }}/recipes/ghostly" -c conda-forge -c openbiosim/label/main --variant-config "${{ github.workspace }}/python_variant.yaml"
62+
#
63+
- name: Build package using rattler-build (dev channel)
6264
if: ${{ github.base_ref != 'main' }}
63-
run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/ghostly/recipes/ghostly
65+
shell: bash
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run: rattler-build build --recipe "${{ github.workspace }}/recipes/ghostly" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"

‎README.md‎

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@@ -30,41 +30,60 @@ See the [examples](examples) directory for more details.
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## Installation
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33-
First create a conda environment using the provided environment file:
33+
### Conda package
34+
35+
Install `ghostly` directly from the `openbiosim` channel:
3436

3537
```
36-
conda env create -f environment.yaml
38+
conda install -c conda-forge -c openbiosim ghostly
3739
```
3840

39-
(We recommend using [Miniforge](https://github.com/conda-forge/miniforge).)
40-
41-
Now install `ghostly` into the environment:
41+
Or, for the development version:
4242

4343
```
44-
conda activate ghostly
45-
pip install .
44+
conda install -c conda-forge -c openbiosim/label/dev ghostly
4645
```
4746

48-
Or, for an editable install (useful for development):
47+
### Installing from source (standalone)
48+
49+
To install from source using [pixi](https://pixi.sh), which will
50+
automatically create an environment with all required dependencies
51+
(including pre-built [Sire](https://github.com/OpenBioSim/sire) and
52+
[BioSimSpace](https://github.com/OpenBioSim/biosimspace)):
4953

5054
```
51-
conda activate ghostly
55+
git clone https://github.com/openbiosim/ghostly
56+
cd ghostly
57+
pixi install
58+
pixi shell
5259
pip install -e .
5360
```
5461

55-
For an existing conda environment, you can also install `ghostly` directly from
56-
the `openbiosim` channel:
62+
### Installing from source (full OpenBioSim development)
63+
64+
If you are developing across the full OpenBioSim stack, first install
65+
[Sire](https://github.com/OpenBioSim/sire) from source by following the
66+
instructions [here](https://github.com/OpenBioSim/sire#installation), then
67+
activate its pixi environment:
5768

5869
```
59-
conda install -c conda-forge -c openbiosim ghostly
70+
pixi shell --manifest-path /path/to/sire/pixi.toml -e dev
6071
```
6172

62-
Or, for the development version:
73+
You may also need to install other packages from source, e.g.
74+
[BioSimSpace](https://github.com/OpenBioSim/biosimspace):
6375

6476
```
65-
conda install -c conda-forge -c openbiosim/label/dev ghostly
77+
pip install -e /path/to/biosimspace/python
78+
```
79+
80+
Then install `ghostly` into the environment:
81+
82+
```
83+
pip install -e .
6684
```
6785

86+
### Testing
6887

6988
You should now have a `ghostly` executable in your path. To test, run:
7089

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