From d084caea961e2382c277cab24a2ed57486fa7daa Mon Sep 17 00:00:00 2001 From: anon Date: Mon, 9 Nov 2026 19:39:27 +0100 Subject: [PATCH] docs: pin install instructions to v0.1.4 v0.1.4 carries the tissue and disease roll-up facets (#73) that the MCP connector's snippets use. Also applies ruff format to tests/test_docs_reference.py. --- README.md | 4 ++-- docs/guides/cli-and-agents.md | 4 ++-- docs/index.md | 6 +++--- docs/reference/mcp.md | 2 +- docs/start.md | 6 +++--- docs/tutorials/00_overview.ipynb | 2 +- tests/test_docs_quickstart.py | 2 +- tests/test_docs_reference.py | 9 ++++++++- 8 files changed, 21 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index 7a49262..b4dac77 100644 --- a/README.md +++ b/README.md @@ -7,10 +7,10 @@ Lean read client for the spatialdata-db spatial-omics collection: query the cata ## Install ```bash -pip install "spatialdata-db @ git+https://github.com/theislab/spatialdata-db-client@v0.1.3" +pip install "spatialdata-db @ git+https://github.com/theislab/spatialdata-db-client@v0.1.4" ``` -This installs the alpha release, v0.1.3. The `main` branch may be ahead of it, and you get the newest code if you leave out `@v0.1.3`. +This installs the alpha release, v0.1.4. The `main` branch may be ahead of it, and you get the newest code if you leave out `@v0.1.4`. ## Usage diff --git a/docs/guides/cli-and-agents.md b/docs/guides/cli-and-agents.md index 07eac18..2040ee5 100644 --- a/docs/guides/cli-and-agents.md +++ b/docs/guides/cli-and-agents.md @@ -5,7 +5,7 @@ The package installs two commands: `sddb-cli`, a thin command line over the cata same catalog. ``` -pip install "spatialdata-db @ git+https://github.com/theislab/spatialdata-db-client@v0.1.3" +pip install "spatialdata-db @ git+https://github.com/theislab/spatialdata-db-client@v0.1.4" ``` ## sddb-cli @@ -122,7 +122,7 @@ A study without an entry in the published `citations.bib` gets a fallback entry The MCP server speaks stdio and exposes the catalog to an agent. Install the extra: ``` -pip install "spatialdata-db[mcp] @ git+https://github.com/theislab/spatialdata-db-client@v0.1.3" +pip install "spatialdata-db[mcp] @ git+https://github.com/theislab/spatialdata-db-client@v0.1.4" ``` ### Claude Desktop diff --git a/docs/index.md b/docs/index.md index a2ed2b4..8c059ae 100644 --- a/docs/index.md +++ b/docs/index.md @@ -29,19 +29,19 @@ The `sddb-cli` command and the `sddb-mcp` server give the shell and AI agents th :::{tab-item} pip ```bash -pip install "spatialdata-db @ git+https://github.com/theislab/spatialdata-db-client@v0.1.3" +pip install "spatialdata-db @ git+https://github.com/theislab/spatialdata-db-client@v0.1.4" ``` ::: :::{tab-item} uv ```bash -uv pip install "spatialdata-db @ git+https://github.com/theislab/spatialdata-db-client@v0.1.3" +uv pip install "spatialdata-db @ git+https://github.com/theislab/spatialdata-db-client@v0.1.4" ``` ::: :::: -This installs the alpha release, v0.1.3. The `main` branch may be ahead of it, and you get the newest code if you leave out `@v0.1.3`. +This installs the alpha release, v0.1.4. The `main` branch may be ahead of it, and you get the newest code if you leave out `@v0.1.4`. The client needs Python 3.12 or newer. It is not on PyPI yet, so install it from GitHub. diff --git a/docs/reference/mcp.md b/docs/reference/mcp.md index d7aff8b..6f0a446 100644 --- a/docs/reference/mcp.md +++ b/docs/reference/mcp.md @@ -3,7 +3,7 @@ `sddb-mcp` serves the catalog to agents over stdio (Model Context Protocol). It needs the optional extra: ```bash -pip install "spatialdata-db[mcp] @ git+https://github.com/theislab/spatialdata-db-client@v0.1.3" +pip install "spatialdata-db[mcp] @ git+https://github.com/theislab/spatialdata-db-client@v0.1.4" sddb-mcp ``` diff --git a/docs/start.md b/docs/start.md index 4a5d2de..5075a6a 100644 --- a/docs/start.md +++ b/docs/start.md @@ -6,16 +6,16 @@ The [DB website]({{ site_url }}) is the place to find data. This page shows what ## Install ```bash -pip install "spatialdata-db @ git+https://github.com/theislab/spatialdata-db-client@v0.1.3" +pip install "spatialdata-db @ git+https://github.com/theislab/spatialdata-db-client@v0.1.4" ``` or, with uv: ```bash -uv pip install "spatialdata-db @ git+https://github.com/theislab/spatialdata-db-client@v0.1.3" +uv pip install "spatialdata-db @ git+https://github.com/theislab/spatialdata-db-client@v0.1.4" ``` -This installs the alpha release, v0.1.3. The `main` branch may be ahead of it, and you get the newest code if you leave out `@v0.1.3`. The package needs Python 3.12 or newer. It is not on PyPI yet, so install it from GitHub. The name `sddb` on PyPI belongs to an unrelated package. +This installs the alpha release, v0.1.4. The `main` branch may be ahead of it, and you get the newest code if you leave out `@v0.1.4`. The package needs Python 3.12 or newer. It is not on PyPI yet, so install it from GitHub. The name `sddb` on PyPI belongs to an unrelated package. The client keeps its cache in the user cache directory of the platform, in a folder called `sddb`. Set `SDDB_CACHE_DIR` to put it somewhere else, for example on a larger disk. The first call to `Catalog()` downloads the catalog (under 10 MB) from a GitHub release. Later calls check for a newer catalog and download it again only when one has been published. diff --git a/docs/tutorials/00_overview.ipynb b/docs/tutorials/00_overview.ipynb index eb5ad8d..c6bcff0 100644 --- a/docs/tutorials/00_overview.ipynb +++ b/docs/tutorials/00_overview.ipynb @@ -21,7 +21,7 @@ "tutorials use.\n", "\n", "```bash\n", - "pip install \"spatialdata-db[viz] @ git+https://github.com/theislab/spatialdata-db-client@v0.1.3\"\n", + "pip install \"spatialdata-db[viz] @ git+https://github.com/theislab/spatialdata-db-client@v0.1.4\"\n", "```\n", "\n", "The tutorials download about 50 MB of data in total, into the cache described in {doc}`02_load_and_inspect`.\n", diff --git a/tests/test_docs_quickstart.py b/tests/test_docs_quickstart.py index eb60ec6..b9f794f 100644 --- a/tests/test_docs_quickstart.py +++ b/tests/test_docs_quickstart.py @@ -8,7 +8,7 @@ _ROOT = Path(__file__).parent.parent # The release the install instructions pin. To bump: replace the old tag in README.md and docs/, then change this line. -ALPHA_TAG = "v0.1.3" +ALPHA_TAG = "v0.1.4" def test_quickstart_api_exists(): diff --git a/tests/test_docs_reference.py b/tests/test_docs_reference.py index 23aed1c..f37c25c 100644 --- a/tests/test_docs_reference.py +++ b/tests/test_docs_reference.py @@ -30,7 +30,14 @@ def test_mcp_page_lists_all_tools(): def test_mcp_page_lists_tool_parameters(): text = (REF / "mcp.md").read_text() - for fn in (tools.query_tool, tools.describe_tool, tools.genes_tool, tools.facets_tool, tools.cite_tool, tools.download_tool): + for fn in ( + tools.query_tool, + tools.describe_tool, + tools.genes_tool, + tools.facets_tool, + tools.cite_tool, + tools.download_tool, + ): for param in inspect.signature(fn).parameters: if param in {"catalog_url", "bib_url", "workers", "facets"}: # internal / not exposed by server.py continue