From 05fce8953c78889b9864e0a68f0bd76815834234 Mon Sep 17 00:00:00 2001 From: Martin Kim Date: Wed, 31 Jan 2024 09:40:41 -0800 Subject: [PATCH] Rename scvi-v2 to mrvi --- README.md | 24 ++++++++++++------------ docs/api.md | 12 ++++++------ docs/conf.py | 2 +- docs/developer_docs.md | 6 +++--- docs/notebooks/example.ipynb | 4 ++-- pyproject.toml | 10 +++++----- src/{scvi_v2 => mrvi}/__init__.py | 2 +- src/{scvi_v2 => mrvi}/_components.py | 0 src/{scvi_v2 => mrvi}/_constants.py | 0 src/{scvi_v2 => mrvi}/_model.py | 0 src/{scvi_v2 => mrvi}/_module.py | 0 src/{scvi_v2 => mrvi}/_tree_utils.py | 0 src/{scvi_v2 => mrvi}/_types.py | 0 src/{scvi_v2 => mrvi}/_utils.py | 0 tests/test_basic.py | 4 ++-- tests/test_components.py | 2 +- tests/test_model.py | 2 +- tests/test_utils.py | 2 +- 18 files changed, 35 insertions(+), 35 deletions(-) rename src/{scvi_v2 => mrvi}/__init__.py (90%) rename src/{scvi_v2 => mrvi}/_components.py (100%) rename src/{scvi_v2 => mrvi}/_constants.py (100%) rename src/{scvi_v2 => mrvi}/_model.py (100%) rename src/{scvi_v2 => mrvi}/_module.py (100%) rename src/{scvi_v2 => mrvi}/_tree_utils.py (100%) rename src/{scvi_v2 => mrvi}/_types.py (100%) rename src/{scvi_v2 => mrvi}/_utils.py (100%) diff --git a/README.md b/README.md index 98cf8bf..135b63d 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,11 @@ -# scvi-v2 +# mrvi [![Tests][badge-tests]][link-tests] [![Documentation][badge-docs]][link-docs] -[badge-tests]: https://img.shields.io/github/workflow/status/justjhong/scvi-v2/Test/main -[link-tests]: https://github.com/YosefLab/scvi-v2/actions/workflows/test.yml -[badge-docs]: https://img.shields.io/readthedocs/scvi-v2 +[badge-tests]: https://img.shields.io/github/workflow/status/justjhong/mrvi/Test/main +[link-tests]: https://github.com/YosefLab/mrvi/actions/workflows/test.yml +[badge-docs]: https://img.shields.io/readthedocs/mrvi V2 of single-cell Variational Inference. @@ -20,20 +20,20 @@ Please refer to the [documentation][link-docs]. In particular, the You need to have Python 3.8 or newer installed on your system. If you don't have Python installed, we recommend installing [Miniconda](https://docs.conda.io/en/latest/miniconda.html). -There are several alternative options to install scvi-v2: +There are several alternative options to install mrvi: 1. Install the latest development version: ```bash -pip install git+https://github.com/justjhong/scvi-v2.git@main +pip install git+https://github.com/justjhong/mrvi.git@main ``` ## Release notes @@ -50,7 +50,7 @@ If you found a bug, please use the [issue tracker][issue-tracker]. > t.b.a [scverse-discourse]: https://discourse.scverse.org/ -[issue-tracker]: https://github.com/justjhong/scvi-v2/issues -[changelog]: https://scvi-v2.readthedocs.io/latest/changelog.html -[link-docs]: https://scvi-v2.readthedocs.io -[link-api]: https://scvi-v2.readthedocs.io/latest/api.html +[issue-tracker]: https://github.com/justjhong/mrvi/issues +[changelog]: https://mrvi.readthedocs.io/latest/changelog.html +[link-docs]: https://mrvi.readthedocs.io +[link-api]: https://mrvi.readthedocs.io/latest/api.html diff --git a/docs/api.md b/docs/api.md index e2497ff..ddd16d0 100644 --- a/docs/api.md +++ b/docs/api.md @@ -3,8 +3,8 @@ ## Preprocessing ```{eval-rst} -.. module:: scvi_v2.pp -.. currentmodule:: scvi_v2 +.. module:: mrvi.pp +.. currentmodule:: mrvi .. autosummary:: :toctree: generated @@ -15,8 +15,8 @@ ## Tools ```{eval-rst} -.. module:: scvi_v2.tl -.. currentmodule:: scvi_v2 +.. module:: mrvi.tl +.. currentmodule:: mrvi .. autosummary:: :toctree: generated @@ -27,8 +27,8 @@ ## Plotting ```{eval-rst} -.. module:: scvi_v2.pl -.. currentmodule:: scvi_v2 +.. module:: mrvi.pl +.. currentmodule:: mrvi .. autosummary:: :toctree: generated diff --git a/docs/conf.py b/docs/conf.py index ca4a721..a4e662d 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -16,7 +16,7 @@ # -- Project information ----------------------------------------------------- -info = metadata("scvi-v2") +info = metadata("mrvi") project_name = info["Name"] author = info["Author"] copyright = f"{datetime.now():%Y}, {author}." diff --git a/docs/developer_docs.md b/docs/developer_docs.md index ca8742e..3f8cbe0 100644 --- a/docs/developer_docs.md +++ b/docs/developer_docs.md @@ -159,7 +159,7 @@ In `pyproject.toml` add the following changes, and you are good to go! [project] - name = "scvi-v2" + name = "mrvi" -version = "0.3.1dev" +dynamic = ["version"] @@ -168,7 +168,7 @@ In `pyproject.toml` add the following changes, and you are good to go! +source = "vcs" + [tool.coverage.run] - source = ["scvi-v2"] + source = ["mrvi"] omit = [ ``` @@ -191,7 +191,7 @@ In addition to the packages needed to _use_ this package, you need additional py the documentation_. It's easy to install them using `pip`: ```bash -pip install "scvi-v2[dev,test,doc]" +pip install "mrvi[dev,test,doc]" ``` ### Code-style diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb index b6b9b12..b43c211 100644 --- a/docs/notebooks/example.ipynb +++ b/docs/notebooks/example.ipynb @@ -15,7 +15,7 @@ "source": [ "import numpy as np\n", "from anndata import AnnData\n", - "import scvi_v2" + "import mrvi" ] }, { @@ -51,7 +51,7 @@ } ], "source": [ - "scvi_v2.pp.basic_preproc(adata)" + "mrvi.pp.basic_preproc(adata)" ] } ], diff --git a/pyproject.toml b/pyproject.toml index 55299b2..afdeaaf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ requires = ["hatchling"] [project] -name = "scvi-v2" +name = "mrvi" version = "0.0.1" description = "Multi-resolution Variational Inference" readme = "README.md" @@ -16,9 +16,9 @@ authors = [ maintainers = [ {name = "Justin Hong", email = "justin.hong@columbia.edu"}, ] -urls.Documentation = "https://scvi-v2.readthedocs.io/" -urls.Source = "https://github.com/YosefLab/scvi-v2" -urls.Home-page = "https://github.com/YosefLab/scvi-v2" +urls.Documentation = "https://mrvi.readthedocs.io/" +urls.Source = "https://github.com/YosefLab/mrvi" +urls.Home-page = "https://github.com/YosefLab/mrvi" dependencies = [ "scvi-tools>=1.0.0", "seaborn>=0.12.1", @@ -47,7 +47,7 @@ test = [ ] [tool.coverage.run] -source = ["scvi_v2"] +source = ["mrvi"] omit = [ "**/test_*.py", ] diff --git a/src/scvi_v2/__init__.py b/src/mrvi/__init__.py similarity index 90% rename from src/scvi_v2/__init__.py rename to src/mrvi/__init__.py index cbe8928..25b98f1 100644 --- a/src/scvi_v2/__init__.py +++ b/src/mrvi/__init__.py @@ -15,4 +15,4 @@ "permutation_test", ] -__version__ = version("scvi-v2") +__version__ = version("mrvi") diff --git a/src/scvi_v2/_components.py b/src/mrvi/_components.py similarity index 100% rename from src/scvi_v2/_components.py rename to src/mrvi/_components.py diff --git a/src/scvi_v2/_constants.py b/src/mrvi/_constants.py similarity index 100% rename from src/scvi_v2/_constants.py rename to src/mrvi/_constants.py diff --git a/src/scvi_v2/_model.py b/src/mrvi/_model.py similarity index 100% rename from src/scvi_v2/_model.py rename to src/mrvi/_model.py diff --git a/src/scvi_v2/_module.py b/src/mrvi/_module.py similarity index 100% rename from src/scvi_v2/_module.py rename to src/mrvi/_module.py diff --git a/src/scvi_v2/_tree_utils.py b/src/mrvi/_tree_utils.py similarity index 100% rename from src/scvi_v2/_tree_utils.py rename to src/mrvi/_tree_utils.py diff --git a/src/scvi_v2/_types.py b/src/mrvi/_types.py similarity index 100% rename from src/scvi_v2/_types.py rename to src/mrvi/_types.py diff --git a/src/scvi_v2/_utils.py b/src/mrvi/_utils.py similarity index 100% rename from src/scvi_v2/_utils.py rename to src/mrvi/_utils.py diff --git a/tests/test_basic.py b/tests/test_basic.py index fb3f226..830322e 100644 --- a/tests/test_basic.py +++ b/tests/test_basic.py @@ -1,9 +1,9 @@ +import mrvi import pytest -import scvi_v2 def test_package_has_version(): - _ = scvi_v2.__version__ + _ = mrvi.__version__ @pytest.mark.skip(reason="This decorator should be removed when test passes.") diff --git a/tests/test_components.py b/tests/test_components.py index 94fc923..843c26c 100644 --- a/tests/test_components.py +++ b/tests/test_components.py @@ -1,6 +1,6 @@ import jax import jax.numpy as jnp -from scvi_v2._components import ( +from mrvi._components import ( AttentionBlock, ConditionalNormalization, Dense, diff --git a/tests/test_model.py b/tests/test_model.py index 429d74d..d2f9409 100644 --- a/tests/test_model.py +++ b/tests/test_model.py @@ -1,8 +1,8 @@ from tempfile import TemporaryDirectory import numpy as np +from mrvi import MrVI from scvi.data import synthetic_iid -from scvi_v2 import MrVI def test_mrvi(): diff --git a/tests/test_utils.py b/tests/test_utils.py index cd1b4ae..8e57007 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -1,5 +1,5 @@ import numpy as np -from scvi_v2._utils import compute_statistic, permutation_test +from mrvi._utils import compute_statistic, permutation_test from sklearn.metrics import pairwise_distances