uv docs

Signed-off-by: zethson <lukas.heumos@posteo.net>
theislab · Nov 28, 2024 · 7d0a672 · 7d0a672
1 parent 67fedbf
commit 7d0a672
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Showing 3 changed files with 14 additions and 17 deletions.
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -3,16 +3,13 @@ build:
     os: ubuntu-22.04
     tools:
         python: "3.11"
-    jobs:
-        pre_build:
-            - python -c "import ehrapy"
-            - pip freeze
-        post_create_environment:
-            - pip install uv
-        post_install:
-            # VIRTUAL_ENV needs to be set manually for now.
-            # See https://github.com/readthedocs/readthedocs.org/pull/11152/
-            - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH pip install .[docs]
+    commands:
+        - asdf plugin add uv
+        - asdf install uv latest
+        - asdf global uv latest
+        - uv venv
+        - uv pip install .[docs]
+        - .venv/bin/python -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html
 sphinx:
     configuration: docs/conf.py
     fail_on_warning: false

diff --git a/docs/tutorials/notebooks b/docs/tutorials/notebooks
diff --git a/pyproject.toml b/pyproject.toml
@@ -7,7 +7,7 @@ name = "ehrapy"
 version = "0.9.0"
 description = "Electronic Health Record Analysis with Python."
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10,<3.13"
 license = {file = "LICENSE"}
 authors = [
     {name = "Lukas Heumos"},
@@ -38,7 +38,6 @@ classifiers = [
     "Operating System :: MacOS :: MacOS X",
     "Operating System :: POSIX :: Linux",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
@@ -66,7 +65,6 @@ dependencies = [
     "fknni",
     "python-dateutil",
     "filelock",
-    "numpy<2.0.0"  # for compatiblity with lifelines
 ]
 
 [project.optional-dependencies]
@@ -101,8 +99,7 @@ docs = [
     "nbsphinx-link",
     "ipykernel",
     "ipython",
-    "medcat",
-    "ehrapy[dask]",
+    "ehrapy[dask,medcat]",
 ]
 test = [
     "ehrapy[dask]",
@@ -135,7 +132,10 @@ markers = [
 filterwarnings = [
     "ignore::DeprecationWarning",
     "ignore::anndata.OldFormatWarning:",
-    "ignore:X converted to numpy array with dtype object:UserWarning"
+    "ignore:X converted to numpy array with dtype object:UserWarning",
+    "ignore:`flavor='seurat_v3'` expects raw count data, but non-integers were found:UserWarning",
+    "ignore:All-NaN slice encountered:RuntimeWarning",
+    "ignore:Observation names are not unique. To make them unique, call `.obs_names_make_unique`.:UserWarning"
 ]
 minversion = 6.0
 norecursedirs = [ '.*', 'build', 'dist', '*.egg', 'data', '__pycache__']
+95 −10		ehrapy_introduction.ipynb
+1 −1		mimic_2_causal_inference.ipynb
+8 −8		mimic_2_fate.ipynb
+1 −1		mimic_2_survival_analysis.ipynb
+87 −9		out_of_core.ipynb
+0 −24		patient_trajectory.ipynb