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Merged
rugeli merged 10 commits into from
May 6, 2026
Merged

Maint/deprecate requirements txt #467

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b0341bf
remove requirements.txt related code
rugeli Apr 27, 2026
fc7af09
update pyproject.toml
rugeli Apr 27, 2026
027dba2
generate new uv file
rugeli Apr 27, 2026
865fc69
update pip install for dockerfile
rugeli Apr 27, 2026
be5f707
use uv sync
rugeli Apr 27, 2026
1d088d0
move server dep list under dependency-groups
rugeli Apr 27, 2026
ae9c4e4
update docker
rugeli Apr 27, 2026
d00c05c
fix path and use uv sync
rugeli Apr 27, 2026
6cd0829
add pydantic to pyproject toml
rugeli May 6, 2026
058338c
update lock file
rugeli May 6, 2026
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112 changes: 0 additions & 112 deletions .github/workflows/make-requirements.yml
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5 changes: 2 additions & 3 deletions README.md
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Expand Up @@ -19,15 +19,14 @@ An algorithm to pack molecular recipes
git clone [email protected]:mesoscope/cellpack.git
cd cellpack
```
1. Create a new virtual environment and activate it.
3. Create a new virtual environment and activate it.
```bash
python -m venv .venv
source .venv/bin/activate
```
1. Install the required packages for your operating system. Replace `linux` with `macos` or `windows` as appropriate.
4. Install the package and its dependencies from `pyproject.toml`.
```bash
pip install --upgrade pip
pip install -r requirements/linux/requirements.txt
pip install -e .
```

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4 changes: 3 additions & 1 deletion docker/Dockerfile.ecs
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Expand Up @@ -4,7 +4,9 @@ WORKDIR /cellpack
COPY . /cellpack

RUN python -m pip install --upgrade pip --root-user-action=ignore
RUN python -m pip install . -r requirements/linux/requirements.txt --root-user-action=ignore
RUN python -m pip install uv --root-user-action=ignore
RUN uv sync --no-default-groups --group server --frozen
ENV PATH="/cellpack/.venv/bin:$PATH"
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@rugeli rugeli Apr 27, 2026

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initially I used pip install ".[server]", but that resolves fresh from PyPI on each build which means rebuilds could pick up different versions. Switching to uv sync keeps the install pinned to uv.lock, giving us more consistent builds.

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@ascibisz ascibisz Apr 30, 2026

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just tried running this locally and it worked perfectly!


EXPOSE 80

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7 changes: 3 additions & 4 deletions docs/CONTRIBUTING.md
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Expand Up @@ -15,12 +15,11 @@ Ready to contribute? Here's how to set up `cellpack` for local development.
git clone [email protected]:{your_name_here}/cellpack.git
```

3. Install the project in editable mode by following installation instructions [here](./docs/INSTALL.md). (It is also recommended to work in a virtual environment):
3. Install the project in editable mode by following installation instructions [here](./INSTALLATION.md). (It is also recommended to work in a virtual environment):

```bash
cd cellpack/
pip install -r requirements/linux/requirements.txt
pip install -e .[dev]
uv sync
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@rugeli rugeli Apr 27, 2026 •
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to address copilot's review comment(slightly out of scope): pip install -e .[dev] has been silently failing on main since the dev lives in [dependency-groups] and pip's [extra] syntax can't read. Switched the contributor setup to use uv sync instead.

```

4. Create a branch for local development:
Expand Down Expand Up @@ -51,7 +50,7 @@ Ready to contribute? Here's how to set up `cellpack` for local development.

### Contributing cheat sheet

1. `pip install -e .[dev]`
1. `uv sync`

This will install your package in editable mode with all the required development
dependencies (i.e. `tox`).
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5 changes: 4 additions & 1 deletion pyproject.toml
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Expand Up @@ -30,6 +30,7 @@ dependencies = [
"pandas",
"plotly",
"pycollada",
"pydantic",
"pymunk",
"python-dotenv",
"rtree",
Expand Down Expand Up @@ -79,6 +80,9 @@ docs = [
"linkify-it-py",
"myst-parser",
]
server = [
"aiohttp",
]

[build-system]
requires = ["uv_build>=0.8.14,<0.9.0"]
Expand All @@ -96,7 +100,6 @@ source-include = [
"docker",
"docs",
"examples",
"requirements",
".dockerignore",
"tests",
"__init__.py",
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