wip!

.readthedocs.yml

@@ -5,4 +5,7 @@ sphinx:
 python:
   version: 3.6
   install:
-    - requirements: .readthedocs-requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - dev

devel/doc

@@ -12,8 +12,8 @@ main() {
 }
 
 rebuild() {
-    pipenv run make clean
-    pipenv run make dirhtml
+    make clean
+    make dirhtml
 
     pushd _build/dirhtml
         kill %

devel/setup-venv

@@ -0,0 +1,11 @@
+#!/bin/bash
+set -euo pipefail
+
+base="$(realpath "$(dirname "$0")/..")"
+venv="$base/.venv"
+
+set -x
+rm -rf "$venv"
+python3.6 -m venv "$venv"
+"$venv"/bin/pip install --upgrade pip setuptools wheel pip-tools
+"$venv"/bin/pip install -e '.[dev]'

devel/venv-run

@@ -0,0 +1,7 @@
+#!/bin/bash
+set -eou pipefail
+
+base="$(realpath "$(dirname "$0")/..")"
+
+source "$base/.venv/bin/activate"
+exec "$@"

doc/development.md

@@ -17,24 +17,36 @@ Versions for this project follow the [Semantic Versioning rules][].
 
 ## Setup
 
-You can use [Pipenv](https://pipenv.pypa.io) to spin up an isolated development
-environment:
+Setup an isolated development environment in `.venv/` with:
 
-    pipenv sync --dev
-    pipenv run nextstrain --help
+    ./devel/setup-venv
 
-The Pipenv development environment includes our dev tools (described below):
+Activate the venv to run any of the commands below:
 
-    pipenv run pytest           # runs doctests as well as mypy and flake8
-    pipenv run mypy nextstrain
-    pipenv run flake8
+    source .venv/bin/activate
+
+(Or alternatively, run the commands below via `./devel/venv-run …`.)
+
+Now test that you can run:
+
+    nextstrain --help
+
+The development environment includes our dev tools (described below):
+
+    pytest           # runs doctests as well as mypy and flake8
+    mypy nextstrain
+    flake8
 
 ## Running with local changes
 
-From within a clone of the git repository you can run `./bin/nextstrain` to
-test your local changes without installing them.  (Note that `./bin/nextstrain`
-is not the script that gets installed by pip as `nextstrain`; that script is
-generated by the `entry_points` configuration in `setup.py`.)
+The project is installed into editable mode when using the venv setup above, so
+any changes you make during development will be used automatically.
+
+If you need to run with local changes in setups without editable mode, you can
+run `./bin/nextstrain` to test your local changes without installing them.
+(Note that `./bin/nextstrain` is not the script that gets installed by pip as
+`nextstrain`; that script is generated by the `entry_points` configuration in
+`setup.py`.)
 
 ## Releasing
 

setup.py

@@ -127,7 +127,7 @@ def find_namespaced_packages(namespace):
             "pytest-mypy",
             "recommonmark",
             "sphinx>=3",
-            "sphinx-argparse",
+            "sphinx-argparse ~=0.3",
             "sphinx-markdown-tables",
             "sphinx_rtd_theme",
             "types-setuptools",