pyvark 0.1.0__tar.gz

pyvark-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Mark Fiers
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pyvark-0.1.0/PKG-INFO

@@ -0,0 +1,171 @@
+Metadata-Version: 2.4
+Name: pyvark
+Version: 0.1.0
+Summary: Python REST client for the Anthive single-cell RNA-seq browser (sibling of the Go `vark` CLI)
+Author-email: Mark Fiers <mark.fiers@kuleuven.be>
+License: MIT
+Project-URL: Homepage, https://codeberg.org/mfiers/pyvark
+Project-URL: Repository, https://codeberg.org/mfiers/pyvark
+Project-URL: Go CLI, https://codeberg.org/mfiers/vark
+Project-URL: Bug Tracker, https://codeberg.org/mfiers/pyvark/issues
+Keywords: bioinformatics,single-cell,rna-seq,anthive,rest-client
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: requests>=2.25.0
+Provides-Extra: pandas
+Requires-Dist: pandas>=1.3.0; extra == "pandas"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
+Requires-Dist: pandas>=1.3.0; extra == "dev"
+Dynamic: license-file
+
+<p align="center"><img src="https://codeberg.org/mfiers/pyvark/raw/branch/main/doc/logo.png" alt="pyvark" width="200"></p>
+
+# pyvark
+
+Python client for the [Anthive](https://codeberg.org/mfiers/anthive4)
+single-cell RNA-seq REST API. Sibling of the Go [`vark`](https://codeberg.org/mfiers/vark)
+CLI — same backend, two front ends.
+
+API surface verified against **anthive REST API 2.7.2** (2026-06-20).
+
+## Why the dual name?
+
+The Go CLI ships as a binary called `vark`. To avoid clobbering it on
+the user's `$PATH` and to keep the PyPI / Codeberg slug obvious, the
+**distribution name** is `pyvark` but the **importable name** is `vark`.
+
+```sh
+pip install pyvark                                    # distribution
+python -c "from vark import AnthiveClient; print('ok')"   # usage
+```
+
+(Both CLI and library live next to each other in the same Anthive setup
+with no shell collision: `vark` = the Go binary, `vark` = the Python
+import.)
+
+## Install
+
+From Codeberg (no PyPI publish yet):
+
+```sh
+pip install git+ssh://git@codeberg.org/mfiers/pyvark.git
+```
+
+Editable from a local checkout:
+
+```sh
+git clone ssh://git@codeberg.org/mfiers/pyvark.git
+cd pyvark
+pip install -e .
+# with pandas for `format='dataframe'` support:
+pip install -e ".[pandas]"
+```
+
+Pyodide / JupyterLite:
+
+```python
+import micropip
+await micropip.install("pyvark")
+from vark import AnthiveClient
+client = AnthiveClient()   # auto-detects {origin}/api/ in the browser
+```
+
+## Minimal example
+
+```python
+from vark import AnthiveClient
+
+client = AnthiveClient(
+    "https://my.anthive.example/api",
+    auth=("user", "password"),
+)
+
+# What's on this server?
+print(client.get_version()["version"])
+databases = client.get_databases()
+print(f"{len(databases)} datasets available")
+
+# Pick a dataset and show its metadata fields
+info = client.get_database_info(databases[0]["id"])
+print(info["title"], info["n_cells"], "cells")
+
+# Render a UMAP scatter server-side and write the PNG
+plot = client.get_plot(
+    info["id"], "scatter",
+    color="cell_type",
+    palette_categorical="tab20",
+    width=6, height=5, dpi=150,
+)
+open("umap.png", "wb").write(plot["bytes"])
+
+# The X-Plot-Caption header carries anthive's prose figure legend —
+# this is the ONLY place the multi-sentence caption exists.
+print(plot["caption"])
+```
+
+## API coverage (highlights)
+
+* `get_root`, `get_health`, `get_metrics`, `get_version`,
+  `get_changelog` — version + latency telemetry (`/health` exposes
+  `mean_response_ms` / `p50_response_ms` / `n_samples`).
+* `get_databases`, `get_database_info`, `get_group(group_id)` —
+  catalog + per-collection landing-page data (API 2.5+).
+* `get_plot(db_id, geom, ...)` — every server-side geom: `scatter`,
+  `hexbin`, `kde2d`, `violin`, `box`, `bar`, `histogram`, `ecdf`,
+  `kde`, `heatmap`, `rolling`, `volcano`, `ma`, `forest`, `de_heatmap`.
+  Captures the `X-Plot-Caption` response header (the multi-sentence
+  figure legend — API 2.7.2+). Supports `color_scale=auto|sequential|
+  divergent`, plot clamps (`log2fc_clip`, `neglog10p_clip`,
+  `logmean_clip`), bar `group_by`, hexbin auto-clip
+  (`vmin_quantile` / `vmax_quantile`), per-axis transforms
+  (`transform_x` / `transform_y`, `asinh_scale`), KDE knobs
+  (`kde_n`, `kde_bw`, `n_levels`, `iso_overlay`, `point_overlay`),
+  marginals / regline overlays. Data export via `format="csv"` /
+  `"tsv"` returns the dataframe the plot was built from (API 2.6+).
+* `list_de_studies`, `get_de_study`, `list_de_contrasts`,
+  `get_de_rows`, `get_de_by_gene` — DE data flow (API 2.3+).
+* `analytics_schema`, `analytics_query`, `analytics_viz` —
+  SELECT-only SQL sandbox + Parquet-backed visualisation.
+* `module_score`, `list_module_scores` — on-the-fly and pre-computed
+  module scores.
+* `list_genesets`, `get_geneset`, `rescan_genesets`.
+* `pick_fastest(base_urls, ...)` — server-selection helper that
+  consumes `/health` latency telemetry.
+
+## Tests
+
+```sh
+# Offline (no server needed):
+uv run --with pytest --with requests python -m pytest tests/test_offline.py -v
+
+# Live smoke (round-trip):
+ANTHIVE_TEST_URL=https://my.anthive/api \
+ANTHIVE_TEST_USER=user ANTHIVE_TEST_PASSWORD=pass \
+uv run --with pytest --with requests --with pandas \
+    python -m pytest tests/test_smoke.py -v
+```
+
+## Versioning
+
+`pyvark` starts at **0.1.0** as a clean break from the legacy
+`antclient` 1.x history that previously lived under
+`anthive4/antclient/`. The Anthive REST API uses its own semver
+(`X.Y.Z`) — see `client.AnthiveClient.API_TARGET` for the version this
+release was last verified against.
+
+## License
+
+MIT — see `LICENSE`.

pyvark-0.1.0/README.md

@@ -0,0 +1,138 @@
+<p align="center"><img src="https://codeberg.org/mfiers/pyvark/raw/branch/main/doc/logo.png" alt="pyvark" width="200"></p>
+
+# pyvark
+
+Python client for the [Anthive](https://codeberg.org/mfiers/anthive4)
+single-cell RNA-seq REST API. Sibling of the Go [`vark`](https://codeberg.org/mfiers/vark)
+CLI — same backend, two front ends.
+
+API surface verified against **anthive REST API 2.7.2** (2026-06-20).
+
+## Why the dual name?
+
+The Go CLI ships as a binary called `vark`. To avoid clobbering it on
+the user's `$PATH` and to keep the PyPI / Codeberg slug obvious, the
+**distribution name** is `pyvark` but the **importable name** is `vark`.
+
+```sh
+pip install pyvark                                    # distribution
+python -c "from vark import AnthiveClient; print('ok')"   # usage
+```
+
+(Both CLI and library live next to each other in the same Anthive setup
+with no shell collision: `vark` = the Go binary, `vark` = the Python
+import.)
+
+## Install
+
+From Codeberg (no PyPI publish yet):
+
+```sh
+pip install git+ssh://git@codeberg.org/mfiers/pyvark.git
+```
+
+Editable from a local checkout:
+
+```sh
+git clone ssh://git@codeberg.org/mfiers/pyvark.git
+cd pyvark
+pip install -e .
+# with pandas for `format='dataframe'` support:
+pip install -e ".[pandas]"
+```
+
+Pyodide / JupyterLite:
+
+```python
+import micropip
+await micropip.install("pyvark")
+from vark import AnthiveClient
+client = AnthiveClient()   # auto-detects {origin}/api/ in the browser
+```
+
+## Minimal example
+
+```python
+from vark import AnthiveClient
+
+client = AnthiveClient(
+    "https://my.anthive.example/api",
+    auth=("user", "password"),
+)
+
+# What's on this server?
+print(client.get_version()["version"])
+databases = client.get_databases()
+print(f"{len(databases)} datasets available")
+
+# Pick a dataset and show its metadata fields
+info = client.get_database_info(databases[0]["id"])
+print(info["title"], info["n_cells"], "cells")
+
+# Render a UMAP scatter server-side and write the PNG
+plot = client.get_plot(
+    info["id"], "scatter",
+    color="cell_type",
+    palette_categorical="tab20",
+    width=6, height=5, dpi=150,
+)
+open("umap.png", "wb").write(plot["bytes"])
+
+# The X-Plot-Caption header carries anthive's prose figure legend —
+# this is the ONLY place the multi-sentence caption exists.
+print(plot["caption"])
+```
+
+## API coverage (highlights)
+
+* `get_root`, `get_health`, `get_metrics`, `get_version`,
+  `get_changelog` — version + latency telemetry (`/health` exposes
+  `mean_response_ms` / `p50_response_ms` / `n_samples`).
+* `get_databases`, `get_database_info`, `get_group(group_id)` —
+  catalog + per-collection landing-page data (API 2.5+).
+* `get_plot(db_id, geom, ...)` — every server-side geom: `scatter`,
+  `hexbin`, `kde2d`, `violin`, `box`, `bar`, `histogram`, `ecdf`,
+  `kde`, `heatmap`, `rolling`, `volcano`, `ma`, `forest`, `de_heatmap`.
+  Captures the `X-Plot-Caption` response header (the multi-sentence
+  figure legend — API 2.7.2+). Supports `color_scale=auto|sequential|
+  divergent`, plot clamps (`log2fc_clip`, `neglog10p_clip`,
+  `logmean_clip`), bar `group_by`, hexbin auto-clip
+  (`vmin_quantile` / `vmax_quantile`), per-axis transforms
+  (`transform_x` / `transform_y`, `asinh_scale`), KDE knobs
+  (`kde_n`, `kde_bw`, `n_levels`, `iso_overlay`, `point_overlay`),
+  marginals / regline overlays. Data export via `format="csv"` /
+  `"tsv"` returns the dataframe the plot was built from (API 2.6+).
+* `list_de_studies`, `get_de_study`, `list_de_contrasts`,
+  `get_de_rows`, `get_de_by_gene` — DE data flow (API 2.3+).
+* `analytics_schema`, `analytics_query`, `analytics_viz` —
+  SELECT-only SQL sandbox + Parquet-backed visualisation.
+* `module_score`, `list_module_scores` — on-the-fly and pre-computed
+  module scores.
+* `list_genesets`, `get_geneset`, `rescan_genesets`.
+* `pick_fastest(base_urls, ...)` — server-selection helper that
+  consumes `/health` latency telemetry.
+
+## Tests
+
+```sh
+# Offline (no server needed):
+uv run --with pytest --with requests python -m pytest tests/test_offline.py -v
+
+# Live smoke (round-trip):
+ANTHIVE_TEST_URL=https://my.anthive/api \
+ANTHIVE_TEST_USER=user ANTHIVE_TEST_PASSWORD=pass \
+uv run --with pytest --with requests --with pandas \
+    python -m pytest tests/test_smoke.py -v
+```
+
+## Versioning
+
+`pyvark` starts at **0.1.0** as a clean break from the legacy
+`antclient` 1.x history that previously lived under
+`anthive4/antclient/`. The Anthive REST API uses its own semver
+(`X.Y.Z`) — see `client.AnthiveClient.API_TARGET` for the version this
+release was last verified against.
+
+## License
+
+MIT — see `LICENSE`.

pyvark-0.1.0/pyproject.toml

@@ -0,0 +1,57 @@
+[build-system]
+requires = ["setuptools>=64", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pyvark"
+version = "0.1.0"
+description = "Python REST client for the Anthive single-cell RNA-seq browser (sibling of the Go `vark` CLI)"
+readme = "README.md"
+requires-python = ">=3.9"
+license = { text = "MIT" }
+authors = [
+    { name = "Mark Fiers", email = "mark.fiers@kuleuven.be" },
+]
+keywords = [
+    "bioinformatics",
+    "single-cell",
+    "rna-seq",
+    "anthive",
+    "rest-client",
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "requests>=2.25.0",
+]
+
+[project.optional-dependencies]
+pandas = ["pandas>=1.3.0"]
+dev = [
+    "pytest>=7.0.0",
+    "pytest-cov>=4.0.0",
+    "pandas>=1.3.0",
+]
+
+[project.urls]
+Homepage      = "https://codeberg.org/mfiers/pyvark"
+Repository    = "https://codeberg.org/mfiers/pyvark"
+"Go CLI"      = "https://codeberg.org/mfiers/vark"
+"Bug Tracker" = "https://codeberg.org/mfiers/pyvark/issues"
+
+[tool.setuptools]
+packages = ["vark"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]

pyvark-0.1.0/pyvark.egg-info/PKG-INFO

@@ -0,0 +1,171 @@
+Metadata-Version: 2.4
+Name: pyvark
+Version: 0.1.0
+Summary: Python REST client for the Anthive single-cell RNA-seq browser (sibling of the Go `vark` CLI)
+Author-email: Mark Fiers <mark.fiers@kuleuven.be>
+License: MIT
+Project-URL: Homepage, https://codeberg.org/mfiers/pyvark
+Project-URL: Repository, https://codeberg.org/mfiers/pyvark
+Project-URL: Go CLI, https://codeberg.org/mfiers/vark
+Project-URL: Bug Tracker, https://codeberg.org/mfiers/pyvark/issues
+Keywords: bioinformatics,single-cell,rna-seq,anthive,rest-client
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: requests>=2.25.0
+Provides-Extra: pandas
+Requires-Dist: pandas>=1.3.0; extra == "pandas"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
+Requires-Dist: pandas>=1.3.0; extra == "dev"
+Dynamic: license-file
+
+<p align="center"><img src="https://codeberg.org/mfiers/pyvark/raw/branch/main/doc/logo.png" alt="pyvark" width="200"></p>
+
+# pyvark
+
+Python client for the [Anthive](https://codeberg.org/mfiers/anthive4)
+single-cell RNA-seq REST API. Sibling of the Go [`vark`](https://codeberg.org/mfiers/vark)
+CLI — same backend, two front ends.
+
+API surface verified against **anthive REST API 2.7.2** (2026-06-20).
+
+## Why the dual name?
+
+The Go CLI ships as a binary called `vark`. To avoid clobbering it on
+the user's `$PATH` and to keep the PyPI / Codeberg slug obvious, the
+**distribution name** is `pyvark` but the **importable name** is `vark`.
+
+```sh
+pip install pyvark                                    # distribution
+python -c "from vark import AnthiveClient; print('ok')"   # usage
+```
+
+(Both CLI and library live next to each other in the same Anthive setup
+with no shell collision: `vark` = the Go binary, `vark` = the Python
+import.)
+
+## Install
+
+From Codeberg (no PyPI publish yet):
+
+```sh
+pip install git+ssh://git@codeberg.org/mfiers/pyvark.git
+```
+
+Editable from a local checkout:
+
+```sh
+git clone ssh://git@codeberg.org/mfiers/pyvark.git
+cd pyvark
+pip install -e .
+# with pandas for `format='dataframe'` support:
+pip install -e ".[pandas]"
+```
+
+Pyodide / JupyterLite:
+
+```python
+import micropip
+await micropip.install("pyvark")
+from vark import AnthiveClient
+client = AnthiveClient()   # auto-detects {origin}/api/ in the browser
+```
+
+## Minimal example
+
+```python
+from vark import AnthiveClient
+
+client = AnthiveClient(
+    "https://my.anthive.example/api",
+    auth=("user", "password"),
+)
+
+# What's on this server?
+print(client.get_version()["version"])
+databases = client.get_databases()
+print(f"{len(databases)} datasets available")
+
+# Pick a dataset and show its metadata fields
+info = client.get_database_info(databases[0]["id"])
+print(info["title"], info["n_cells"], "cells")
+
+# Render a UMAP scatter server-side and write the PNG
+plot = client.get_plot(
+    info["id"], "scatter",
+    color="cell_type",
+    palette_categorical="tab20",
+    width=6, height=5, dpi=150,
+)
+open("umap.png", "wb").write(plot["bytes"])
+
+# The X-Plot-Caption header carries anthive's prose figure legend —
+# this is the ONLY place the multi-sentence caption exists.
+print(plot["caption"])
+```
+
+## API coverage (highlights)
+
+* `get_root`, `get_health`, `get_metrics`, `get_version`,
+  `get_changelog` — version + latency telemetry (`/health` exposes
+  `mean_response_ms` / `p50_response_ms` / `n_samples`).
+* `get_databases`, `get_database_info`, `get_group(group_id)` —
+  catalog + per-collection landing-page data (API 2.5+).
+* `get_plot(db_id, geom, ...)` — every server-side geom: `scatter`,
+  `hexbin`, `kde2d`, `violin`, `box`, `bar`, `histogram`, `ecdf`,
+  `kde`, `heatmap`, `rolling`, `volcano`, `ma`, `forest`, `de_heatmap`.
+  Captures the `X-Plot-Caption` response header (the multi-sentence
+  figure legend — API 2.7.2+). Supports `color_scale=auto|sequential|
+  divergent`, plot clamps (`log2fc_clip`, `neglog10p_clip`,
+  `logmean_clip`), bar `group_by`, hexbin auto-clip
+  (`vmin_quantile` / `vmax_quantile`), per-axis transforms
+  (`transform_x` / `transform_y`, `asinh_scale`), KDE knobs
+  (`kde_n`, `kde_bw`, `n_levels`, `iso_overlay`, `point_overlay`),
+  marginals / regline overlays. Data export via `format="csv"` /
+  `"tsv"` returns the dataframe the plot was built from (API 2.6+).
+* `list_de_studies`, `get_de_study`, `list_de_contrasts`,
+  `get_de_rows`, `get_de_by_gene` — DE data flow (API 2.3+).
+* `analytics_schema`, `analytics_query`, `analytics_viz` —
+  SELECT-only SQL sandbox + Parquet-backed visualisation.
+* `module_score`, `list_module_scores` — on-the-fly and pre-computed
+  module scores.
+* `list_genesets`, `get_geneset`, `rescan_genesets`.
+* `pick_fastest(base_urls, ...)` — server-selection helper that
+  consumes `/health` latency telemetry.
+
+## Tests
+
+```sh
+# Offline (no server needed):
+uv run --with pytest --with requests python -m pytest tests/test_offline.py -v
+
+# Live smoke (round-trip):
+ANTHIVE_TEST_URL=https://my.anthive/api \
+ANTHIVE_TEST_USER=user ANTHIVE_TEST_PASSWORD=pass \
+uv run --with pytest --with requests --with pandas \
+    python -m pytest tests/test_smoke.py -v
+```
+
+## Versioning
+
+`pyvark` starts at **0.1.0** as a clean break from the legacy
+`antclient` 1.x history that previously lived under
+`anthive4/antclient/`. The Anthive REST API uses its own semver
+(`X.Y.Z`) — see `client.AnthiveClient.API_TARGET` for the version this
+release was last verified against.
+
+## License
+
+MIT — see `LICENSE`.

pyvark-0.1.0/pyvark.egg-info/SOURCES.txt

@@ -0,0 +1,13 @@
+LICENSE
+README.md
+pyproject.toml
+pyvark.egg-info/PKG-INFO
+pyvark.egg-info/SOURCES.txt
+pyvark.egg-info/dependency_links.txt
+pyvark.egg-info/requires.txt
+pyvark.egg-info/top_level.txt
+tests/test_offline.py
+tests/test_smoke.py
+vark/__init__.py
+vark/client.py
+vark/helpers.py

pyvark-0.1.0/pyvark.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

pyvark-0.1.0/pyvark.egg-info/requires.txt

@@ -0,0 +1,9 @@
+requests>=2.25.0
+
+[dev]
+pytest>=7.0.0
+pytest-cov>=4.0.0
+pandas>=1.3.0
+
+[pandas]
+pandas>=1.3.0

pyvark-0.1.0/pyvark.egg-info/top_level.txt

@@ -0,0 +1 @@
+vark

pyvark-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+