From 674baacf6d27bcdd5705042cdec8cfe2dcbcf1bf Mon Sep 17 00:00:00 2001 From: scverse-bot Date: Tue, 21 May 2024 13:46:06 +0000 Subject: [PATCH 1/5] Update template to v0.4.0 --- .cruft.json | 4 ++-- .github/workflows/test.yaml | 6 +++--- .gitignore | 1 + README.md | 2 +- docs/conf.py | 8 ++++---- docs/conf.py.rej | 8 ++++++++ docs/contributing.md | 2 +- pyproject.toml | 2 +- pyproject.toml.rej | 19 +++++++++++++++++++ 9 files changed, 40 insertions(+), 12 deletions(-) create mode 100644 docs/conf.py.rej create mode 100644 pyproject.toml.rej diff --git a/.cruft.json b/.cruft.json index ac8342c..6cbcd50 100644 --- a/.cruft.json +++ b/.cruft.json @@ -1,7 +1,7 @@ { "template": "https://github.com/scverse/cookiecutter-scverse", - "commit": "586b1652162ff7994b0070a034023d64289ae416", - "checkout": "v0.3.1", + "commit": "87a407a65408d75a949c0b54b19fd287475a56f8", + "checkout": "v0.4.0", "context": { "cookiecutter": { "project_name": "geome", diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index afc0a0d..5a7f674 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -24,11 +24,11 @@ jobs: matrix: include: - os: ubuntu-latest - python: "3.9" + python: "3.10" - os: ubuntu-latest - python: "3.11" + python: "3.12" - os: ubuntu-latest - python: "3.11" + python: "3.12" pip-flags: "--pre" name: PRE-RELEASE DEPENDENCIES diff --git a/.gitignore b/.gitignore index 780ac9f..e86794f 100644 --- a/.gitignore +++ b/.gitignore @@ -18,6 +18,7 @@ __pycache__/ /.pytest_cache/ /.cache/ /data/ +/node_modules/ # docs /docs/generated/ diff --git a/README.md b/README.md index 0e7cad2..f0f4332 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,7 @@ Please refer to the [documentation][link-docs]. In particular, the ## Installation -You need to have Python 3.9 or newer installed on your system. If you don't have +You need to have Python 3.10 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 geome: diff --git a/docs/conf.py b/docs/conf.py index 0734162..36c335f 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,10 +41,10 @@ html_context = { "display_github": True, # Integrate GitHub - "github_user": "tothmarcella", # Username - "github_repo": project_name, # Repo name - "github_version": "main", # Version - "conf_py_path": "/docs/", # Path in the checkout to the docs root + "github_user": "tothmarcella", + "github_repo": "https://github.com/theislab/geome", + "github_version": "main", + "conf_py_path": "/docs/", } # -- General configuration --------------------------------------------------- diff --git a/docs/conf.py.rej b/docs/conf.py.rej new file mode 100644 index 0000000..b0c737b --- /dev/null +++ b/docs/conf.py.rej @@ -0,0 +1,8 @@ +diff a/docs/conf.py b/docs/conf.py (rejected hunks) +@@ -1,5 +1,5 @@ + # Configuration file for the Sphinx documentation builder. +-# ++ + # This file only contains a selection of the most common options. For a full + # list see the documentation: + # https://www.sphinx-doc.org/en/master/usage/configuration.html diff --git a/docs/contributing.md b/docs/contributing.md index cf23234..9d8e3af 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -51,7 +51,7 @@ and [prettier][prettier-editors]. ## Writing tests ```{note} -Remember to first install the package with `pip install '-e[dev,test]'` +Remember to first install the package with `pip install -e '.[dev,test]'` ``` This package uses the [pytest][] for automated testing. Please [write tests][scanpy-test-docs] for every function added diff --git a/pyproject.toml b/pyproject.toml index c0c65ac..41812ec 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -117,7 +117,7 @@ ignore = [ "D107", # Errors from function calls in argument defaults. These are fine when the result is immutable. "B008", - # __magic__ methods are are often self-explanatory, allow missing docstrings + # __magic__ methods are often self-explanatory, allow missing docstrings "D105", # first line should end with a period [Bug: doesn't work with single-line docstrings] "D400", diff --git a/pyproject.toml.rej b/pyproject.toml.rej new file mode 100644 index 0000000..4173e47 --- /dev/null +++ b/pyproject.toml.rej @@ -0,0 +1,19 @@ +diff a/pyproject.toml b/pyproject.toml (rejected hunks) +@@ -7,7 +7,7 @@ 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" +-requires-python = ">=3.9" ++requires-python = ">=3.10" + license = {file = "LICENSE"} + authors = [ + {name = "Marcella Toth"}, +@@ -33,7 +33,7 @@ doc = [ + "docutils>=0.8,!=0.18.*,!=0.19.*", + "sphinx>=4", + "sphinx-book-theme>=1.0.0", +- "myst-nb", ++ "myst-nb>=1.1.0", + "sphinxcontrib-bibtex>=1.0.0", + "sphinx-autodoc-typehints", + "sphinxext-opengraph", From 63c7782d4c43d7ee3d3199f371dc2205b924a2b5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Selman=20=C3=96zleyen?= <32667648+selmanozleyen@users.noreply.github.com> Date: Wed, 3 Jul 2024 17:10:13 +0200 Subject: [PATCH 2/5] Delete docs/conf.py.rej --- docs/conf.py.rej | 8 -------- 1 file changed, 8 deletions(-) delete mode 100644 docs/conf.py.rej diff --git a/docs/conf.py.rej b/docs/conf.py.rej deleted file mode 100644 index b0c737b..0000000 --- a/docs/conf.py.rej +++ /dev/null @@ -1,8 +0,0 @@ -diff a/docs/conf.py b/docs/conf.py (rejected hunks) -@@ -1,5 +1,5 @@ - # Configuration file for the Sphinx documentation builder. --# -+ - # This file only contains a selection of the most common options. For a full - # list see the documentation: - # https://www.sphinx-doc.org/en/master/usage/configuration.html From bb1ffddf2060febb425e2c6fe561a88a95ab64b4 Mon Sep 17 00:00:00 2001 From: selmanozleyen Date: Wed, 3 Jul 2024 17:28:17 +0200 Subject: [PATCH 3/5] update rej files --- pyproject.toml | 4 ++-- pyproject.toml.rej | 19 ------------------- 2 files changed, 2 insertions(+), 21 deletions(-) delete mode 100644 pyproject.toml.rej diff --git a/pyproject.toml b/pyproject.toml index 41812ec..74f8910 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,7 +7,7 @@ name = "geome" version = "0.0.2" description = "Geometric Learning for Genome Data" readme = "README.md" -requires-python = ">=3.9" +requires-python = ">=3.10" license = {file = "LICENSE"} authors = [ {name = "Marcella Toth"}, @@ -49,7 +49,7 @@ doc = [ "furo", "sphinx>=4", "sphinx-book-theme>=1.0.0", - "myst-nb", + "myst-nb>=1.1.0", "sphinxcontrib-bibtex>=1.0.0", "sphinx-autodoc-typehints", # For notebooks diff --git a/pyproject.toml.rej b/pyproject.toml.rej deleted file mode 100644 index 4173e47..0000000 --- a/pyproject.toml.rej +++ /dev/null @@ -1,19 +0,0 @@ -diff a/pyproject.toml b/pyproject.toml (rejected hunks) -@@ -7,7 +7,7 @@ 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" --requires-python = ">=3.9" -+requires-python = ">=3.10" - license = {file = "LICENSE"} - authors = [ - {name = "Marcella Toth"}, -@@ -33,7 +33,7 @@ doc = [ - "docutils>=0.8,!=0.18.*,!=0.19.*", - "sphinx>=4", - "sphinx-book-theme>=1.0.0", -- "myst-nb", -+ "myst-nb>=1.1.0", - "sphinxcontrib-bibtex>=1.0.0", - "sphinx-autodoc-typehints", - "sphinxext-opengraph", From 2f6f9d66e8ea375ec256d61cb373c9df68e65c65 Mon Sep 17 00:00:00 2001 From: selmanozleyen Date: Wed, 3 Jul 2024 17:36:46 +0200 Subject: [PATCH 4/5] update version --- .github/workflows/test.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 5a7f674..294f58d 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -50,7 +50,7 @@ jobs: - name: Install test dependencies run: | python -m pip install --upgrade pip wheel - pip install torch==2.1.0 + pip install torch>=2.1.0 pip install torch-scatter torch-sparse torch-cluster - name: Install dependencies run: | From fa366ae44d41f2111e31dd49002a470bdc518310 Mon Sep 17 00:00:00 2001 From: selmanozleyen Date: Wed, 3 Jul 2024 17:41:27 +0200 Subject: [PATCH 5/5] update --- .github/workflows/test.yaml | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml index 294f58d..2c5dffb 100644 --- a/.github/workflows/test.yaml +++ b/.github/workflows/test.yaml @@ -50,7 +50,7 @@ jobs: - name: Install test dependencies run: | python -m pip install --upgrade pip wheel - pip install torch>=2.1.0 + pip install "torch>=2.1.0" pip install torch-scatter torch-sparse torch-cluster - name: Install dependencies run: | diff --git a/pyproject.toml b/pyproject.toml index 74f8910..86fda59 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,7 +22,7 @@ urls.Source = "https://github.com/theislab/geome" urls.Home-page = "https://github.com/theislab/geome" dependencies = [ "anndata", - "torch", + "torch>=2.1.0", "torch_geometric", "torch_sparse", "torch_cluster",