name change

theislab · May 26, 2023 · ba18951 · ba18951
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diff --git a/.cruft.json b/.cruft.json
@@ -4,13 +4,13 @@
   "checkout": "v0.2.0",
   "context": {
     "cookiecutter": {
-      "project_name": "gpu_spatial_graph_pipeline",
-      "package_name": "gpu_spatial_graph_pipeline",
+      "project_name": "geome",
+      "package_name": "geome",
       "project_description": "The repo provides a set of tools for creating PyTorch Geometric (PyG) data objects from AnnData objects, which are commonly used for storing and manipulating single-cell genomics data. In addition, the repo includes functionality for creating PyTorch Lightning (PyTorch-Lightning) DataModule objects from the PyG data objects, which can be used to create graph neural network (GNN) data pipelines. The PyG data objects represent graphs, where the nodes represent cells and the edges represent relationships between the cells, and can be used to perform GNN tasks such as node classification, graph classification, and link prediction. The repo is written in Python and utilizes the PyTorch, PyTorch Geometric, and PyTorch-Lightning libraries.",
       "author_full_name": "Marcella Toth",
       "author_email": "[email protected]",
       "github_user": "tothmarcella",
-      "project_repo": "https://github.com/theislab/gpu_spatial_graph_pipeline",
+      "project_repo": "https://github.com/theislab/geome",
       "license": "MIT License",
       "_copy_without_render": [
         ".github/workflows/**.yaml",

diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -1,5 +1,5 @@
 name: Feature request
-description: Propose a new feature for gpu_spatial_graph_pipeline
+description: Propose a new feature for geome
 labels: enhancement
 body:
     - type: textarea

diff --git a/README.md b/README.md
@@ -1,9 +1,9 @@
-# gpu_spatial_graph_pipeline
+# geome
 
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
 
-[badge-tests]: https://img.shields.io/github/actions/workflow/status/theislab/gpu-spatial-graph-pipeline/test.yaml?branch=main
+[badge-tests]: https://img.shields.io/github/actions/workflow/status/theislab/geome/test.yaml?branch=main
 [link-tests]: https://github.com/theislab/gpu-spatial_graph-pipeline/actions/workflows/test.yml
 [badge-docs]: https://img.shields.io/readthedocs/gpu-spatial-graph_pipeline
 
@@ -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 [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
 
-There are several alternative options to install gpu_spatial_graph_pipeline:
+There are several alternative options to install geome:
 
 <!--
-1) Install the latest release of `gpu_spatial_graph_pipeline` from `PyPI <https://pypi.org/project/gpu_spatial_graph_pipeline/>`_:
+1) Install the latest release of `geome` from `PyPI <https://pypi.org/project/geome/>`_:
 
 ```bash
-pip install gpu_spatial_graph_pipeline
+pip install geome
 ```
 -->
 
 1. Install the latest development version:
 
 ```bash
-pip install git+https://github.com/theislab/gpu_spatial_graph_pipeline.git@main
+pip install git+https://github.com/theislab/geome.git@main
 ```
 
 ## Release notes
@@ -56,15 +56,15 @@ This project was generated from [@cjolowicz]'s [Hypermodern Python Cookiecutter]
 [@cjolowicz]: https://github.com/cjolowicz
 [pypi]: https://pypi.org/
 [hypermodern python cookiecutter]: https://github.com/cjolowicz/cookiecutter-hypermodern-python
-[file an issue]: https://github.com/theislab/gpu_spatial_graph_pipeline/issues
+[file an issue]: https://github.com/theislab/geome/issues
 [pip]: https://pip.pypa.io/
 
 ## Citation
 
 > t.b.a
 
 [scverse-discourse]: https://discourse.scverse.org/
-[issue-tracker]: https://github.com/theislab/gpu-spatial-graph-pipeline/issues
-[changelog]: https://gpu-spatial-graph-pipeline.readthedocs.io/changelog.html
-[link-docs]: https://gpu-spatial-graph-pipeline.readthedocs.io/
-[link-api]: https://gpu-spatial-graph-pipeline.readthedocs.io/en/latest/api.html
+[issue-tracker]: https://github.com/theislab/geome/issues
+[changelog]: https://geome.readthedocs.io/changelog.html
+[link-docs]: https://geome.readthedocs.io/
+[link-api]: https://geome.readthedocs.io/en/latest/api.html
diff --git a/docs/api.md b/docs/api.md
@@ -3,15 +3,15 @@
 ## AnnData to Data
 
 ```{eval-rst}
-.. automodule:: gpu_spatial_graph_pipeline.anndata2data
+.. automodule:: geome.anndata2data
     :members:
 
 ```
 
 ## Datamodule
 
 ```{eval-rst}
-.. automodule:: gpu_spatial_graph_pipeline.datamodule
+.. automodule:: geome.datamodule
     :members:
 
 ```
diff --git a/docs/conf.py b/docs/conf.py
@@ -20,15 +20,15 @@
 
 # -- Project information -----------------------------------------------------
 
-#info = metadata("gpu_spatial_graph_pipeline")
+#info = metadata("geome")
 #project_name = info["Name"]
-project_name = "gpu_spatial_graph_pipeline"
+project_name = "geome"
 #author = info["Author"]
 author = "Selman Ozleyen, Chelsea Bright, Marcella Toth"
 copyright = f"{datetime.now():%Y}, {author}."
 #version = info["Version"]
 version = "0.1"
-repository_url = f"https://github.com/theislab/gpu-spatial-graph-pipeline"
+repository_url = f"https://github.com/theislab/geome"
 
 # The full version, including alpha/beta/rc tags
 #release = info["Version"]

diff --git a/docs/conf.py.rej b/docs/conf.py.rej
@@ -5,7 +5,7 @@ diff a/docs/conf.py b/docs/conf.py	(rejected hunks)
 
 -# NOTE: If you installed your project in editable mode, this might be stale.
 -#       If this is the case, reinstall it to refresh the metadata
- info = metadata("gpu_spatial_graph_pipeline")
+ info = metadata("geome")
  project_name = info["Name"]
  author = info["Author"]
  copyright = f"{datetime.now():%Y}, {author}."

diff --git a/docs/contributing.md b/docs/contributing.md
@@ -13,7 +13,7 @@ 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
-cd gpu_spatial_graph_pipeline
+cd geome
 pip install -e ".[dev,test,doc]"
 ```
 

diff --git a/docs/notebooks/creating_data_objects_from_anndata.ipynb b/docs/notebooks/creating_data_objects_from_anndata.ipynb
@@ -27,8 +27,8 @@
     "import warnings\n",
     "import anndata as ad\n",
     "import squidpy as sq\n",
-    "from gpu_spatial_graph_pipeline import transforms\n",
-    "from gpu_spatial_graph_pipeline.anndata2data import AnnData2DataByCategory\n",
+    "from geome import transforms\n",
+    "from geome.anndata2data import AnnData2DataByCategory\n",
     "from utils.datasets import DatasetHartmann\n",
     "\n",
     "warnings.filterwarnings('ignore')\n"

diff --git a/docs/notebooks/linear_NCEM_graph.ipynb b/docs/notebooks/linear_NCEM_graph.ipynb
@@ -36,11 +36,11 @@
     "import pytorch_lightning as pl\n",
     "import torch\n",
     "import anndata as ad\n",
-    "from gpu_spatial_graph_pipeline import transforms \n",
-    "from gpu_spatial_graph_pipeline.anndata2data import AnnData2DataByCategory\n",
+    "from geome import transforms \n",
+    "from geome.anndata2data import AnnData2DataByCategory\n",
     "from utils.datasets import DatasetHartmann\n",
     "from utils.models.linear_ncem import LinearNCEM\n",
-    "from gpu_spatial_graph_pipeline.datamodule import GraphAnnDataModule"
+    "from geome.datamodule import GraphAnnDataModule"
    ]
   },
   {
@@ -169,7 +169,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Missing logger folder: /home/marcella/Documents/gpu-spatial-graph-pipeline/docs/notebooks/lightning_logs\n",
+      "Missing logger folder: /home/marcella/Documents/geome/docs/notebooks/lightning_logs\n",
       "\n",
       "  | Name        | Type            | Params\n",
       "------------------------------------------------\n",

diff --git a/docs/notebooks/non_linear_NCEM_graph.ipynb b/docs/notebooks/non_linear_NCEM_graph.ipynb
@@ -36,11 +36,11 @@
     "import pytorch_lightning as pl\n",
     "import torch\n",
     "import anndata as ad\n",
-    "from gpu_spatial_graph_pipeline import transforms\n",
-    "from gpu_spatial_graph_pipeline.anndata2data import AnnData2DataByCategory\n",
+    "from geome import transforms\n",
+    "from geome.anndata2data import AnnData2DataByCategory\n",
     "from utils.datasets import DatasetHartmann\n",
     "from utils.models.non_linear_ncem import NonLinearNCEM\n",
-    "from gpu_spatial_graph_pipeline.datamodule import GraphAnnDataModule\n"
+    "from geome.datamodule import GraphAnnDataModule\n"
    ]
   },
   {

diff --git a/docs/notebooks/utils/models/graph_embedding.py b/docs/notebooks/utils/models/graph_embedding.py
@@ -3,7 +3,7 @@
 g(A,X) from the paper
 """
 import torch
-from gpu_spatial_graph_pipeline.models.modules.graph_ae import GraphAE
+from geome.models.modules.graph_ae import GraphAE
 #from models.modules.graph_ae import GraphAE
 import pytorch_lightning as pl
 from torch_geometric.data import Batch

diff --git a/docs/template_usage.md b/docs/template_usage.md
@@ -19,7 +19,7 @@ cruft create https://github.com/scverse/cookiecutter-scverse
 and you should have :cite:p:`Wolf2018`
 
 ```
-cd gpu_spatial_graph_pipeline
+cd geome
 ```
 
 into the new project directory. Now that you have created a new repository locally, the first step is to push it to github. To do this, you'd have to create a **new repository** on github.
@@ -28,13 +28,13 @@ Since `cruft` already populated the local repository of your project with all th
 If you are familiar with git and knows how to handle git conflicts, you can go ahead with your preferred choice.
 
 :::{note}
-If you are looking at this document in the [cookiecutter-scverse-instance][] repository documentation, throughout this document the name of the project is `cookiecutter-scverse-instance`. Otherwise it should be replaced by your new project name: `gpu_spatial_graph_pipeline`.
+If you are looking at this document in the [cookiecutter-scverse-instance][] repository documentation, throughout this document the name of the project is `cookiecutter-scverse-instance`. Otherwise it should be replaced by your new project name: `geome`.
 :::
 
-Now that your new project repository has been created on github at `https://github.com/tothmarcella/gpu_spatial_graph_pipeline` you can push your first commit to github.
+Now that your new project repository has been created on github at `https://github.com/tothmarcella/geome` you can push your first commit to github.
 To do this, simply follow the instructions on your github repository page or a more verbose walkthrough here:
 
-Assuming you are in `/your/path/to/gpu_spatial_graph_pipeline`. Add all files and commit.
+Assuming you are in `/your/path/to/geome`. Add all files and commit.
 
 ```bash
 # stage all files of your new repo
@@ -59,14 +59,14 @@ Now that all the files of the newly created project have been committed, go ahea
 
 ```bash
 # update the `origin` of your local repo with the remote github link
-git remote add origin https://github.com/tothmarcella/gpu_spatial_graph_pipeline.git
+git remote add origin https://github.com/tothmarcella/geome.git
 # rename the default branch to main
 git branch -M main
 # push all your files to remote
 git push -u origin main
 ```
 
-Your project should be now available at `https://github.com/tothmarcella/gpu_spatial_graph_pipeline`. While the repository at this point can be directly used, there are few remaining steps that needs to be done in order to achieve full functionality.
+Your project should be now available at `https://github.com/tothmarcella/geome`. While the repository at this point can be directly used, there are few remaining steps that needs to be done in order to achieve full functionality.
 
 ### Coverage tests with _Codecov_
 
@@ -90,7 +90,7 @@ While [codecov docs][] has a very extensive documentation on how to get started,
 To set it up, simply go to the [codecov app][] page and follow the instructions to activate it for your repository.
 Once the activation is completed, go back to the `Actions` tab and re-run the failing workflows.
 
-The workflows should now succeed and you will be able to find the code coverage at this link: `https://app.codecov.io/gh/tothmarcella/gpu_spatial_graph_pipeline`. You might have to wait couple of minutes and the coverage of this repository should be ~60%.
+The workflows should now succeed and you will be able to find the code coverage at this link: `https://app.codecov.io/gh/tothmarcella/geome`. You might have to wait couple of minutes and the coverage of this repository should be ~60%.
 
 If your repository is private, you will have to specify an additional token in the repository secrets. In brief, you need to:
 
@@ -291,7 +291,7 @@ In `pyproject.toml` add the following changes, and you are good to go!
 
 
  [project]
- name = "gpu_spatial_graph_pipeline"
+ name = "geome"
 -version = "0.3.1dev"
 +dynamic = ["version"]
 
@@ -300,7 +300,7 @@ In `pyproject.toml` add the following changes, and you are good to go!
 +source = "vcs"
 +
  [tool.coverage.run]
- source = ["gpu_spatial_graph_pipeline"]
+ source = ["geome"]
  omit = [
 ```
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -3,7 +3,7 @@ build-backend = "hatchling.build"
 requires = ["hatchling"]
 
 [project]
-name = "gpu_spatial_graph_pipeline"
+name = "geome"
 version = "0.0.1"
 description = "The repo provides a set of tools for creating PyTorch Geometric (PyG) data objects from AnnData objects, which are commonly used for storing and manipulating single-cell genomics data. In addition, the repo includes functionality for creating PyTorch Lightning (PyTorch-Lightning) DataModule objects from the PyG data objects, which can be used to create graph neural network (GNN) data pipelines. The PyG data objects represent graphs, where the nodes represent cells and the edges represent relationships between the cells, and can be used to perform GNN tasks such as node classification, graph classification, and link prediction. The repo is written in Python and utilizes the PyTorch, PyTorch Geometric, and PyTorch-Lightning libraries."
 readme = "README.md"
@@ -15,9 +15,9 @@ authors = [
 maintainers = [
     {name = "Marcella Toth", email = "[email protected]"},
 ]
-urls.Documentation = "https://gpu_spatial_graph_pipeline.readthedocs.io/"
-urls.Source = "https://github.com/theislab/gpu_spatial_graph_pipeline"
-urls.Home-page = "https://github.com/theislab/gpu_spatial_graph_pipeline"
+urls.Documentation = "https://geome.readthedocs.io/"
+urls.Source = "https://github.com/theislab/geome"
+urls.Home-page = "https://github.com/theislab/geome"
 dependencies = [
     "anndata",
     # for debug logging (referenced from the issue template)
@@ -49,10 +49,10 @@ test = [
 ]
 
 [tool.hatch.build.targets.wheel]
-packages = ['src/gpu_spatial_graph_pipeline']
+packages = ['src/geome']
 
 [tool.coverage.run]
-source = ["gpu_spatial_graph_pipeline"]
+source = ["geome"]
 omit = [
     "**/test_*.py",
 ]

diff --git a/tests/test_basic.py b/tests/test_basic.py
@@ -1,6 +1,6 @@
 import pytest
 
-import gpu_spatial_graph_pipeline
+import geome
 
 
 def test_example():