Update branch names (#1157)

* Update scvelo default branch

Update default branch from `master` to `main`.

* Update `ci.yml`

Update branches triggering CI.

.github/workflows/build.yml

@@ -2,9 +2,9 @@ name: Check Build
 
 on:
     push:
-        branches: [master]
+        branches: [main]
     pull_request:
-        branches: [master]
+        branches: [main]
 
 jobs:
     package:

.github/workflows/ci.yml

@@ -2,9 +2,9 @@ name: CI
 
 on:
     push:
-        branches: [master, develop, "release/**"]
+        branches: [main]
     pull_request:
-        branches: [master, develop, "release/**"]
+        branches: [main]
 
 jobs:
     # Skip CI if commit message contains `[ci skip]` in the subject

CONTRIBUTING.rst

@@ -81,7 +81,7 @@ The docstrings of scVelo largely follow the `numpy`-style. New docstrings should
 Submitting pull requests
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
-New features and bug fixes are added to the code base through a pull request (PR). To implement a feature or bug fix, create a branch from `master`. The existence of bugs suggests insufficient test coverage. As such, bug fixes should, ideally, include a unit test or extend an existing one. Please ensure that
+New features and bug fixes are added to the code base through a pull request (PR). To implement a feature or bug fix, create a branch from `main`. The existence of bugs suggests insufficient test coverage. As such, bug fixes should, ideally, include a unit test or extend an existing one. Please ensure that
 
 - branch names have the prefix `feat/` or `fix/`.
 - your code follows the project conventions.

README.md

@@ -6,7 +6,7 @@
 [link-pypi]: https://pypi.org/project/scvelo
 [badge-pypidownloads]: https://pepy.tech/badge/scvelo
 [link-pypidownloads]: https://pepy.tech/project/scvelo
-[badge-ci]: https://img.shields.io/github/actions/workflow/status/theislab/scvelo/ci.yml?branch=master
+[badge-ci]: https://img.shields.io/github/actions/workflow/status/theislab/scvelo/ci.yml?branch=main
 [link-ci]: https://github.com/theislab/scvelo/actions/workflows/ci.yml
 
 # scVelo - RNA velocity generalized through dynamical modeling

debug.py

@@ -0,0 +1,14 @@
+import numpy as np
+
+import scvelo as scv
+
+adata = scv.datasets.pancreas(file_path="data/pancreas.h5ad")
+obs_names = adata.obs_names.tolist()
+obs_names[0] = f"blah-{obs_names[0]}"
+obs_names[1] = f"blah-{obs_names[0]}"
+adata.obs_names = obs_names
+
+bdata = adata.copy()
+bdata.obs_names = np.arange(0, bdata.n_obs).astype(str)
+
+adata = scv.utils.merge(adata, bdata)

docs/source/_ext/edit_on_github.py

@@ -37,7 +37,7 @@ def html_page_context(app, pagename, templatename, context, doctree):
     # For sphinx_rtd_theme.
     context["display_github"] = True
     context["github_user"] = "theislab"
-    context["github_version"] = "master"
+    context["github_version"] = "main"
     context["github_repo"] = repo
     context["conf_py_path"] = conf_py_path
 

docs/source/conf.py

@@ -135,7 +135,7 @@
       <a href="https://colab.research.google.com/{{ docname|e }}" target="_parent">
       <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/></a>
       <a href="https://nbviewer.jupyter.org/{{ docname|e }}" target="_parent">
-      <img src="https://github.com/theislab/scvelo/raw/master/docs/source/_static/nbviewer-badge.svg" alt="Open In nbviewer"/></a>
+      <img src="https://github.com/theislab/scvelo/raw/main/docs/source/_static/nbviewer-badge.svg" alt="Open In nbviewer"/></a>
     </div>
 """
 
@@ -252,7 +252,7 @@ def get_linenos(obj):
 
 # set project_dir: project/docs/source/conf.py/../../.. → project/
 project_dir = Path(__file__).parent.parent.parent
-github_url_scvelo = "https://github.com/theislab/scvelo/tree/master"
+github_url_scvelo = "https://github.com/theislab/scvelo/tree/main"
 github_url_read_loom = "https://github.com/theislab/anndata/tree/master/anndata"
 github_url_read = "https://github.com/theislab/scanpy/tree/master"
 github_url_scanpy = "https://github.com/theislab/scanpy/tree/master/scanpy"

docs/source/index.rst

@@ -103,7 +103,7 @@ For further information visit `scvelo.org <https://scvelo.org>`_.
 .. |Docs| image:: https://readthedocs.org/projects/scvelo/badge/?version=latest
    :target: https://scvelo.readthedocs.io
 
-.. |travis| image:: https://travis-ci.org/theislab/scvelo.svg?branch=master
+.. |travis| image:: https://travis-ci.org/theislab/scvelo.svg?branch=main
    :target: https://travis-ci.org/theislab/scvelo
 
 .. _Scanpy: https://scanpy.readthedocs.io

scvelo/datasets/_read.py

@@ -0,0 +1,52 @@
+import os
+from pathlib import Path
+from urllib.request import urlretrieve
+
+import numpy as np
+import pandas as pd
+
+
+def load(filename, backup_url=None, header="infer", index_col="infer", **kwargs):
+    """Load a csv, txt, tsv or npy file."""
+    numpy_ext = {"npy", "npz"}
+    pandas_ext = {"csv", "txt", "tsv"}
+
+    if not os.path.exists(filename) and backup_url is None:
+        raise FileNotFoundError(f"Did not find file {filename}.")
+
+    elif not os.path.exists(filename):
+        d = os.path.dirname(filename)
+        if not os.path.exists(d):
+            os.makedirs(d)
+        urlretrieve(backup_url, filename)
+
+    ext = Path(filename).suffixes[-1][1:]
+
+    if ext in numpy_ext:
+        return np.load(filename, **kwargs)
+
+    elif ext in pandas_ext:
+        df = pd.read_csv(
+            filename,
+            header=header,
+            index_col=None if index_col == "infer" else index_col,
+            **kwargs,
+        )
+        if index_col == "infer" and len(df.columns) > 1:
+            is_int_index = all(np.arange(0, len(df)) == df.iloc[:, 0])
+            is_str_index = isinstance(df.iloc[0, 0], str) and all(
+                [not isinstance(d, str) for d in df.iloc[0, 1:]]
+            )
+            if is_int_index or is_str_index:
+                df.set_index(df.columns[0], inplace=True)
+        return df
+
+    else:
+        raise ValueError(
+            f"'{filename}' does not end on a valid extension.\n"
+            "Please, provide one of the available extensions.\n"
+            f"{numpy_ext | pandas_ext}\n"
+        )
+
+
+read_csv = load