Go back to regular pip (#1702)

* Go back to regular flit

Co-authored-by: Isaac Virshup <ivirshup@gmail.com>

.azure-pipelines.yml

@@ -42,7 +42,6 @@ jobs:
 
   - script: |
       python -m pip install --upgrade pip
-      pip install -r .pip-2033.txt
       pip install pytest-cov wheel
       pip install .[dev,doc,test,louvain,leiden,magic,scvi,harmony,scrublet,scanorama]
     displayName: 'Install dependencies'
@@ -96,14 +95,13 @@ jobs:
 
   - script: |
       python -m pip install --upgrade pip
-      pip install setuptools setuptools_scm pytoml wheel twine
-    displayName: 'Install build dependencies'
+      pip install build twine
+    displayName: 'Install build tools and requirements'
 
   - script: pip list
     displayName: 'Display installed versions'
 
   - script: |
-      pip install flit
-      flit build
+      python -m build --sdist --wheel .
       twine check dist/*
     displayName: 'Build & Twine check'

.readthedocs.yml

@@ -6,7 +6,6 @@ sphinx:
 python:
   version: 3.8
   install:
-  - requirements: .pip-2033.txt
   - method: pip
     path: .
     extra_requirements:

docs/installation.rst

@@ -41,28 +41,23 @@ cloned version after you update with `git pull`) call::
 
 .. _on GitHub: https://github.com/theislab/scanpy
 
-.. note::
-
-   Due to a `bug in pip`_, packages installed by `flit` can be uninstalled by normal pip operations.
-   For now, you can avoid this by using::
-
-       pip install -e ".[dev,doc,test]"
-
-.. _bug in pip: https://github.com/pypa/pip/issues/9670
-
 If you want to let conda_ handle the installations of dependencies, do::
 
     pip install beni
     beni pyproject.toml > environment.yml
     conda env create -f environment.yml
     conda activate scanpy
-    flit install -s --deps=develop  # or: pip install -e ".[dev,doc,test]"
+    flit install -s --deps=develop
 
 On Windows, you might have to use `flit install --pth-file`
 if you are not able to give yourself the `create symbolic links`_ privilege.
 
 .. _create symbolic links: https://docs.microsoft.com/en-us/windows/security/threat-protection/security-policy-settings/create-symbolic-links
 
+.. note::
+
+    `pip install -e` still works, but may not in future versions.
+
 Docker
 ~~~~~~
 If you're using Docker_, you can use e.g. the image `gcfntnu/scanpy`_ from Docker Hub.

pyproject.toml

@@ -1,7 +1,7 @@
 [build-system]
 build-backend = 'flit_core.buildapi'
 requires = [
-    'flit_core >=2,<4',
+    'flit_core >=3.1,<4',
     'setuptools_scm',
     'pytoml',
     'importlib_metadata>=0.7; python_version < "3.8"',

setup.py

@@ -62,8 +62,7 @@ def setup_args(config_path=Path("pyproject.toml")):
     if "develop" in sys.argv:
         msg = (
             "Please use `flit install -s` or `flit install --pth-file` "
-            "instead of `pip install -e`/`python setup.py develop` "
-            "once https://github.com/pypa/pip/issues/9670 is fixed."
+            "instead of `pip install -e`/`python setup.py develop`"
         )
     elif "install" in sys.argv:
         msg = 'Please use `pip install "$d"` instead of `python "$d/setup.py" install`'