From ebc0537faf10ec6d714953a6232c7d095bf7b5ab Mon Sep 17 00:00:00 2001 From: Intron7 Date: Fri, 6 Dec 2024 13:36:15 +0100 Subject: [PATCH 01/12] test uv --- .readthedocs.yml | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 1cccce2b..9f7007c4 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -1,16 +1,23 @@ version: 2 submodules: include: all + build: os: ubuntu-24.04 tools: - python: '3.12' + python: "3.12" + commands: + # Install and set up uv + - asdf plugin add uv + - asdf install uv latest + - asdf global uv latest + + # Use uv to synchronize dependencies + - uv sync --extra doc --frozen + + # Build documentation using uv and sphinx + - uv run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html + sphinx: configuration: docs/conf.py fail_on_warning: true -python: - install: - - method: pip - path: . - extra_requirements: - - doc From 13f97dc706c96a7104292498e5c7b872a57c5ce0 Mon Sep 17 00:00:00 2001 From: Intron7 Date: Fri, 6 Dec 2024 13:37:27 +0100 Subject: [PATCH 02/12] test different install --- .readthedocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 9f7007c4..4560d413 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -13,7 +13,7 @@ build: - asdf global uv latest # Use uv to synchronize dependencies - - uv sync --extra doc --frozen + - uv pip install .[doc] # Build documentation using uv and sphinx - uv run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html From 3d637e464f91130ee05a7092367def5fab076a88 Mon Sep 17 00:00:00 2001 From: Intron7 Date: Fri, 6 Dec 2024 13:38:27 +0100 Subject: [PATCH 03/12] add system --- .readthedocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 4560d413..c6d76c9c 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -13,7 +13,7 @@ build: - asdf global uv latest # Use uv to synchronize dependencies - - uv pip install .[doc] + - uv pip install --system .[doc] # Build documentation using uv and sphinx - uv run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html From 8e5d4f079c325950b858580450d6eb00174a89f3 Mon Sep 17 00:00:00 2001 From: Intron7 Date: Fri, 6 Dec 2024 13:41:54 +0100 Subject: [PATCH 04/12] test python3.11 --- .readthedocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index c6d76c9c..4949ef0a 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -5,7 +5,7 @@ submodules: build: os: ubuntu-24.04 tools: - python: "3.12" + python: "3.11" commands: # Install and set up uv - asdf plugin add uv From 9c18bd373f28b4b2722ec322a5ae6d62941bf736 Mon Sep 17 00:00:00 2001 From: Intron7 Date: Fri, 6 Dec 2024 13:44:14 +0100 Subject: [PATCH 05/12] update install --- .readthedocs.yml | 4 ++-- pyproject.toml | 6 ++++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 4949ef0a..cd3aca12 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -5,7 +5,7 @@ submodules: build: os: ubuntu-24.04 tools: - python: "3.11" + python: "3.12" commands: # Install and set up uv - asdf plugin add uv @@ -13,7 +13,7 @@ build: - asdf global uv latest # Use uv to synchronize dependencies - - uv pip install --system .[doc] + - uv pip install --system ".[doc]" # Build documentation using uv and sphinx - uv run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html diff --git a/pyproject.toml b/pyproject.toml index d33bc1d2..1858d5aa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,8 +26,6 @@ dependencies = [ ] [project.optional-dependencies] -rapids11 = ["cupy-cuda11x","cudf-cu11==24.10.*", "cuml-cu11==24.10.*", "cugraph-cu11==24.10.*"] -rapids12 = ["cupy-cuda12x","cudf-cu12==24.10.*", "cuml-cu12==24.10.*", "cugraph-cu12==24.10.*"] doc = [ "sphinx>=4.5.0", "sphinx-copybutton", @@ -38,6 +36,10 @@ doc = [ "sphinx_copybutton", "pytest", ] + +rapids11 = ["cupy-cuda11x","cudf-cu11==24.10.*", "cuml-cu11==24.10.*", "cugraph-cu11==24.10.*"] +rapids12 = ["cupy-cuda12x","cudf-cu12==24.10.*", "cuml-cu12==24.10.*", "cugraph-cu12==24.10.*"] + test = [ "pytest", "profimp", From 5fb49e659c9e2e50a575a260d28d59e70dea8b5f Mon Sep 17 00:00:00 2001 From: Intron7 Date: Fri, 6 Dec 2024 13:46:59 +0100 Subject: [PATCH 06/12] undo toml --- pyproject.toml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 1858d5aa..d33bc1d2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,6 +26,8 @@ dependencies = [ ] [project.optional-dependencies] +rapids11 = ["cupy-cuda11x","cudf-cu11==24.10.*", "cuml-cu11==24.10.*", "cugraph-cu11==24.10.*"] +rapids12 = ["cupy-cuda12x","cudf-cu12==24.10.*", "cuml-cu12==24.10.*", "cugraph-cu12==24.10.*"] doc = [ "sphinx>=4.5.0", "sphinx-copybutton", @@ -36,10 +38,6 @@ doc = [ "sphinx_copybutton", "pytest", ] - -rapids11 = ["cupy-cuda11x","cudf-cu11==24.10.*", "cuml-cu11==24.10.*", "cugraph-cu11==24.10.*"] -rapids12 = ["cupy-cuda12x","cudf-cu12==24.10.*", "cuml-cu12==24.10.*", "cugraph-cu12==24.10.*"] - test = [ "pytest", "profimp", From 3fca0f264f5fcd75527e8d04f9e4fda8e184dcdb Mon Sep 17 00:00:00 2001 From: Intron7 Date: Fri, 6 Dec 2024 13:57:37 +0100 Subject: [PATCH 07/12] test hatch env --- .readthedocs.yml | 2 +- hatch.toml | 11 +++++++++++ pyproject.toml | 9 --------- 3 files changed, 12 insertions(+), 10 deletions(-) create mode 100644 hatch.toml diff --git a/.readthedocs.yml b/.readthedocs.yml index cd3aca12..9f7007c4 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -13,7 +13,7 @@ build: - asdf global uv latest # Use uv to synchronize dependencies - - uv pip install --system ".[doc]" + - uv sync --extra doc --frozen # Build documentation using uv and sphinx - uv run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html diff --git a/hatch.toml b/hatch.toml new file mode 100644 index 00000000..7d11867b --- /dev/null +++ b/hatch.toml @@ -0,0 +1,11 @@ +[envs.default] +installer = "uv" +features = ["dev"] + +[envs.hatch-test] +features = ["test", "rapids12"] + +[envs.docs] +features = ["doc"] +scripts.build = "sphinx-build -M html docs docs/_build {args}" +scripts.clean = "git clean -fXd docs" diff --git a/pyproject.toml b/pyproject.toml index d33bc1d2..acb60ac9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -101,15 +101,6 @@ markers = [ "gpu: tests that use a GPU (currently unused, but needs to be specified here as we import anndata.tests.helpers, which uses it)", ] -[tool.hatch.envs.hatch-test] -features = ["test", "rapids12"] - -[tool.hatch.envs.docs] -installer = "uv" -features = ["doc"] -scripts.build = "sphinx-build -M html docs docs/_build {args}" -scripts.clean = "git clean -fXd docs" - [tool.hatch.build] # exclude big files that don’t need to be installed exclude = [ From 5c0f79b0d4b16fdcdad00be6f48d98d189ef6c0b Mon Sep 17 00:00:00 2001 From: Intron7 Date: Fri, 6 Dec 2024 14:04:11 +0100 Subject: [PATCH 08/12] test without frozen --- .readthedocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 9f7007c4..54d1bbdd 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -13,7 +13,7 @@ build: - asdf global uv latest # Use uv to synchronize dependencies - - uv sync --extra doc --frozen + - uv sync --extra doc # Build documentation using uv and sphinx - uv run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html From 21774b0bc4ced1ab6fe929ea816f1151017062db Mon Sep 17 00:00:00 2001 From: Intron7 Date: Fri, 6 Dec 2024 14:06:33 +0100 Subject: [PATCH 09/12] last test --- .readthedocs.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 54d1bbdd..6df3cf0d 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -13,10 +13,10 @@ build: - asdf global uv latest # Use uv to synchronize dependencies - - uv sync --extra doc + - uv pip install .[doc] # Build documentation using uv and sphinx - - uv run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html + - python run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html sphinx: configuration: docs/conf.py From 36ea626c42a28f4e9a7b32dffb7b5c9d2922ec87 Mon Sep 17 00:00:00 2001 From: Intron7 Date: Fri, 6 Dec 2024 14:07:16 +0100 Subject: [PATCH 10/12] add system --- .readthedocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 6df3cf0d..4df5b795 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -13,7 +13,7 @@ build: - asdf global uv latest # Use uv to synchronize dependencies - - uv pip install .[doc] + - uv pip install --system .[doc] # Build documentation using uv and sphinx - python run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html From 8b2c81668493d2bceea1c9fee33814dbfa991c49 Mon Sep 17 00:00:00 2001 From: Intron7 Date: Fri, 6 Dec 2024 14:11:18 +0100 Subject: [PATCH 11/12] update command --- .readthedocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 4df5b795..93b01185 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -16,7 +16,7 @@ build: - uv pip install --system .[doc] # Build documentation using uv and sphinx - - python run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html + - python -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html sphinx: configuration: docs/conf.py From fe7a48ad00a9d071965dbae287b6b59d7618e839 Mon Sep 17 00:00:00 2001 From: "Philipp A." Date: Tue, 10 Dec 2024 11:46:10 +0100 Subject: [PATCH 12/12] adjust comment --- .readthedocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index 93b01185..668b1931 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -15,7 +15,7 @@ build: # Use uv to synchronize dependencies - uv pip install --system .[doc] - # Build documentation using uv and sphinx + # Build documentation using sphinx - python -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html sphinx: