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ElliottKasoarElliottKasoar
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Deprecate extras (#672)
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‎.github/workflows/ci-dev.yml‎

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@@ -22,7 +22,7 @@ jobs:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: uv sync --extra all
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run: uv sync --extra chgnet --extra dpa3 --extra d3 --extra grace --extra mace --extra orb --extra pet-mad --extra plumed
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# Full reinstall in case the version number is the same as the last release
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- name: Uninstall release versions

‎.github/workflows/ci.yml‎

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@@ -25,7 +25,7 @@ jobs:
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uv cache clean
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- name: Install "all" dependencies
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run: uv sync --extra all
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run: uv sync --extra chgnet --extra dpa3 --extra d3 --extra grace --extra mace --extra orb --extra pet-mad --extra plumed
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- name: Install PLUMED
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uses: Iximiel/install-plumed@v1
@@ -51,7 +51,7 @@ jobs:
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- name: Install updated e3nn dependencies
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run: |
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uv cache clean
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uv sync --extra mattersim --extra fairchem-1 --extra sevennet --extra nequip --extra d3
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uv sync --extra mattersim --extra fairchem --extra sevennet --extra nequip --extra d3
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uv pip install --reinstall pynvml
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uv pip install fairchem-core[torch-extras] --no-build-isolation
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@@ -62,32 +62,6 @@ jobs:
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HF_TOKEN: ${{ secrets.HF_TOKEN }}
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run: uv run --no-sync pytest tests/test_{mlip_calculators,single_point}.py
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- name: Install dgl dependencies
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run: |
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uv cache clean
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uv sync --extra mace --extra m3gnet --extra alignn --extra d3
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uv pip install --reinstall pynvml
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- name: Run test suite for dgl dependencies
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env:
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# show timings of tests
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PYTEST_ADDOPTS: "--durations=0"
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run: uv run --no-sync pytest tests/test_{mlip_calculators,single_point,eos}.py
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- name: Install UMA
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run: |
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uv cache clean
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uv sync --extra fairchem-2
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uv pip install --reinstall pynvml
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uv pip install fairchem-core --no-build-isolation
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- name: Run test suite for UMA
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env:
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# show timings of tests
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PYTEST_ADDOPTS: "--durations=0"
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HF_TOKEN: ${{ secrets.HF_TOKEN }}
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run: uv run --no-sync pytest tests/test_{mlip_calculators,single_point}.py
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- name: Report coverage to Coveralls
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uses: coverallsapp/github-action@v2
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with:

‎.github/workflows/mac.yml‎

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@@ -21,7 +21,7 @@ jobs:
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python-version: ${{ matrix.python-version }}
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- name: Install "all" dependencies
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run: uv sync --extra all
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run: uv sync --extra chgnet --extra dpa3 --extra d3 --extra grace --extra mace --extra orb --extra pet-mad --extra plumed
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- name: Install PLUMED
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uses: Iximiel/install-plumed@v1
@@ -46,7 +46,7 @@ jobs:
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- name: Install updated e3nn dependencies
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run: |
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uv sync --extra mattersim --extra fairchem-1 --extra sevennet --extra nequip --extra d3
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uv sync --extra mattersim --extra fairchem --extra sevennet --extra nequip --extra d3
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uv pip install --reinstall pynvml
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uv pip install "fairchem-core[torch-extras]" --no-build-isolation
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@@ -56,27 +56,3 @@ jobs:
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PYTEST_ADDOPTS: "--durations=0"
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HF_TOKEN: ${{ secrets.HF_TOKEN }}
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run: uv run --no-sync pytest tests/test_{mlip_calculators,single_point}.py
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- name: Install dgl dependencies
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run: |
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uv sync --extra mace --extra m3gnet --extra alignn --extra d3
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uv pip install --reinstall pynvml
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- name: Run test suite for dgl dependencies
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env:
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# show timings of tests
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PYTEST_ADDOPTS: "--durations=0"
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run: uv run --no-sync pytest tests/test_{mlip_calculators,single_point,eos}.py
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- name: Install UMA
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run: |
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uv sync --extra fairchem-2
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uv pip install --reinstall pynvml
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uv pip install fairchem-core --no-build-isolation
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- name: Run test suite for UMA
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env:
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# show timings of tests
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PYTEST_ADDOPTS: "--durations=0"
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HF_TOKEN: ${{ secrets.HF_TOKEN }}
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run: uv run --no-sync pytest tests/test_{mlip_calculators,single_point}.py

‎.github/workflows/windows.yml‎

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@@ -25,7 +25,7 @@ jobs:
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prune-cache: false
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- name: Install "all" dependencies
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run: uv sync --extra all
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run: uv sync --extra chgnet --extra dpa3 --extra d3 --extra grace --extra mace
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- name: Download extra models
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shell: bash
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- name: Install updated e3nn dependencies
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run: |
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uv sync --extra fairchem-1 --extra sevennet --extra nequip
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uv sync --extra fairchem --extra sevennet --extra nequip
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uv pip install --reinstall pynvml
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uv pip install "fairchem-core[torch-extras]" --no-build-isolation
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‎README.md‎

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Original file line numberDiff line numberDiff line change
@@ -57,12 +57,6 @@ python3 -m pip install janus-core[mace,chgnet,sevennet]
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> for more details.
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To install all MLIPs currently compatible with MACE, run:
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```python
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python3 -m pip install janus-core[all]
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```
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Individual `extras` are listed in [Getting Started](https://stfc.github.io/janus-core/user_guide/get_started.html#installation), as well as in [pyproject.toml](pyproject.toml) under `[project.optional-dependencies]`.
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@@ -82,17 +76,13 @@ Current and planned features include:
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- [x] Support for multiple MLIPs
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- MACE
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- M3GNet
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- CHGNet
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- ALIGNN
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- SevenNet
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- NequIP
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- DPA3
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- Orb
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- MatterSim
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- GRACE
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- EquiformerV2
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- eSEN
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- UMA
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- PET-MAD
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- [x] Single point calculations
@@ -245,66 +235,67 @@ prints the following:
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```shell
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Usage: janus singlepoint [OPTIONS]
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Perform single point calculations and save to file.
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╭─ Options ───────────────────────────────────────────────────────────────────────────╮
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│ --config TEXT Path to configuration file. │
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│ --help Show this message and exit. │
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╰─────────────────────────────────────────────────────────────────────────────────────╯
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╭─ MLIP calculator ───────────────────────────────────────────────────────────────────╮
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│ * --arch [mace|mace_mp|mace_off|m3gne MLIP architecture to use for │
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│ t|chgnet|alignn|sevennet|neq calculations. │
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│ uip|dpa3|orb|mattersim|grace [required] │
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│ |esen|equiformer|pet_mad|uma │
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│ |mace_omol] │
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│ --device [cpu|cuda|mps|xpu] Device to run calculations │
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│ on. │
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│ [default: cpu] │
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│ --model TEXT MLIP model name, or path to │
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│ model. │
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│ --calc-kwargs DICT Keyword arguments to pass to │
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│ selected calculator. Must be │
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│ passed as a dictionary │
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│ wrapped in quotes, e.g. │
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│ "{'key': value}". │
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╰─────────────────────────────────────────────────────────────────────────────────────╯
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╭─ Calculation ───────────────────────────────────────────────────────────────────────╮
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│ * --struct PATH Path of structure to simulate. │
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│ [required] │
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│ --properties [energy|stress|forces|hessia Properties to calculate. If │
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│ n] not specified, 'energy', │
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│ 'forces' and 'stress' will be │
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│ returned. │
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│ --out PATH Path to save structure with │
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│ calculated results. Default is │
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│ inferred from `file_prefix`. │
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╰─────────────────────────────────────────────────────────────────────────────────────╯
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╭─ Structure I/O ─────────────────────────────────────────────────────────────────────╮
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│ --file-prefix PATH Prefix for output files, including directories. Default │
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│ directory is ./janus_results, and default filename │
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│ prefix is inferred from the input stucture filename. │
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│ --read-kwargs DICT Keyword arguments to pass to ase.io.read. Must be │
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│ passed as a dictionary wrapped in quotes, e.g. "{'key': │
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│ value}". By default, read_kwargs['index'] = ':', so all │
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│ structures are read. │
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│ --write-kwargs DICT Keyword arguments to pass to ase.io.write when saving │
292-
│ any structures. Must be passed as a dictionary wrapped │
293-
│ in quotes, e.g. "{'key': value}". │
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╰─────────────────────────────────────────────────────────────────────────────────────╯
295-
╭─ Logging/summary ───────────────────────────────────────────────────────────────────╮
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│ --log PATH Path to save logs to. Default is │
297-
│ inferred from `file_prefix` │
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│ --tracker --no-tracker Whether to save carbon emissions of │
299-
│ calculation │
300-
│ [default: tracker] │
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│ --summary PATH Path to save summary of inputs, │
302-
│ start/end time, and carbon emissions. │
303-
│ Default is inferred from │
304-
│ `file_prefix`. │
305-
│ --progress-bar --no-progress-bar Whether to show progress bar. │
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│ [default: progress-bar] │
307-
╰─────────────────────────────────────────────────────────────────────────────────────╯
238+
Perform single point calculations and save to file.
239+
240+
╭─ Options ────────────────────────────────────────────────────────────────────────╮
241+
│ --config TEXT Path to configuration file. │
242+
│ --help Show this message and exit. │
243+
╰──────────────────────────────────────────────────────────────────────────────────╯
244+
╭─ MLIP calculator ────────────────────────────────────────────────────────────────╮
245+
│ * --arch [mace|mace_mp|mace_off|chg MLIP architecture to use for │
246+
│ net|sevennet|nequip|dpa3|o calculations. │
247+
│ rb|mattersim|grace|pet_mad [required] │
248+
│ |fairchem|mace_omol] │
249+
│ --device [cpu|cuda|mps|xpu] Device to run calculations │
250+
│ on. │
251+
│ [default: cpu] │
252+
│ --model TEXT MLIP model name, or path to │
253+
│ model. │
254+
│ --calc-kwargs DICT Keyword arguments to pass to │
255+
│ selected calculator. Must be │
256+
│ passed as a dictionary │
257+
│ wrapped in quotes, e.g. │
258+
│ "{'key': value}". │
259+
╰──────────────────────────────────────────────────────────────────────────────────╯
260+
╭─ Calculation ────────────────────────────────────────────────────────────────────╮
261+
│ * --struct PATH Path of structure to │
262+
│ simulate. │
263+
│ [required] │
264+
│ --properties [energy|stress|forces|hessi Properties to calculate. If │
265+
│ an] not specified, 'energy', │
266+
│ 'forces' and 'stress' will │
267+
│ be returned. │
268+
│ --out PATH Path to save structure with │
269+
│ calculated results. Default │
270+
│ is inferred from │
271+
│ `file_prefix`. │
272+
╰──────────────────────────────────────────────────────────────────────────────────╯
273+
╭─ Structure I/O ──────────────────────────────────────────────────────────────────╮
274+
│ --file-prefix PATH Prefix for output files, including directories. │
275+
│ Default directory is ./janus_results, and default │
276+
│ filename prefix is inferred from the input stucture │
277+
│ filename. │
278+
│ --read-kwargs DICT Keyword arguments to pass to ase.io.read. Must be │
279+
│ passed as a dictionary wrapped in quotes, e.g. │
280+
│ "{'key': value}". By default, read_kwargs['index'] = │
281+
│ ':', so all structures are read. │
282+
│ --write-kwargs DICT Keyword arguments to pass to ase.io.write when │
283+
│ saving any structures. Must be passed as a │
284+
│ dictionary wrapped in quotes, e.g. "{'key': value}". │
285+
╰──────────────────────────────────────────────────────────────────────────────────╯
286+
╭─ Logging/summary ────────────────────────────────────────────────────────────────╮
287+
│ --log PATH Path to save logs to. Default is │
288+
│ inferred from `file_prefix` │
289+
│ --tracker --no-tracker Whether to save carbon emissions of │
290+
│ calculation │
291+
│ [default: tracker] │
292+
│ --summary PATH Path to save summary of inputs, │
293+
│ start/end time, and carbon │
294+
│ emissions. Default is inferred from │
295+
│ `file_prefix`. │
296+
│ --progress-bar --no-progress-bar Whether to show progress bar. │
297+
│ [default: progress-bar] │
298+
╰──────────────────────────────────────────────────────────────────────────────────╯
308299
```
309300

310301

@@ -403,7 +394,7 @@ We recommend installing uv for dependency management when developing for `janus-
403394
```shell
404395
git clone https://github.com/stfc/janus-core
405396
cd janus-core
406-
uv sync --extra all # Create a virtual environment and install dependencies
397+
uv sync --extra chgnet --extra d3 --extra mace --extra orb # Create a virtual environment and install dependencies
407398
source .venv/bin/activate
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pre-commit install # Install pre-commit hooks
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pytest -v # Discover and run all tests

‎containers/Dockerfile.marimo‎

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@@ -49,7 +49,7 @@ RUN uv pip install --no-cache-dir marimo[recommended,lsp,sql] altair pandas pyth
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openai \
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nbformat \
5151
pytest
52-
RUN uv pip install --no-cache-dir 'janus-core[all]@git+https://github.com/stfc/janus-core.git@main'
52+
RUN uv pip install --no-cache-dir 'janus-core[chgnet,dpa3,d3,grace,mace,orb,pet-mad,plumed]@git+https://github.com/stfc/janus-core.git@main'
5353
RUN uv pip install --no-cache-dir cuequivariance==0.5.1 \
5454
cuequivariance-torch==0.6.1 \
5555
cuequivariance-ops-torch-cu12==0.6.1 \

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