Merge branch 'main' into latent-repi

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 release of `scvi-v2` from `PyPI <https://pypi.org/project/scvi-v2/>`_:
+1) Install the latest release of `mrvi` from `PyPI <https://pypi.org/project/mrvi/>`_:
 
 ```bash
-pip install scvi-v2
+pip 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

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

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}."

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

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)"
    ]
   }
  ],

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 = "[email protected]"},
 ]
-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>=1.1.0rc2",
     "seaborn>=0.12.1",
@@ -47,7 +47,7 @@ test = [
 ]
 
 [tool.coverage.run]
-source = ["scvi_v2"]
+source = ["mrvi"]
 omit = [
     "**/test_*.py",
 ]

src/scvi_v2/__init__.py → src/mrvi/__init__.py

@@ -15,4 +15,4 @@
     "permutation_test",
 ]
 
-__version__ = version("scvi-v2")
+__version__ = version("mrvi")

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.")

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,

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():

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