discotoolkit 1.2.1__tar.gz → 1.2.2__tar.gz

{discotoolkit-1.2.1 → discotoolkit-1.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: discotoolkit
-Version: 1.2.1
+Version: 1.2.2
 Summary: DISCOtoolkit is an python package that allows users to access data and use the tools provided by the DISCO database.
 Home-page: https://disco.bii.a-star.edu.sg/
 Author: Li Mengwei, Rom Uddamvathanak
@@ -43,7 +43,7 @@ Dynamic: summary
 -->
 [![Documentation](https://img.shields.io/badge/docs-disco.bii.a--star.edu.sg-blue)](https://disco.bii.a-star.edu.sg/v1/docs/toolkit/guide/) [![Downloads](https://static.pepy.tech/personalized-badge/discotoolkit?period=total&units=international_system&left_color=black&right_color=orange&left_text=Downloads)](https://pepy.tech/project/discotoolkit) [![PyPI version](https://img.shields.io/pypi/v/discotoolkit)](https://pypi.org/project/discotoolkit)
 
-# DISCOtoolkit 1.2.1
+# DISCOtoolkit 1.2.2
 
 DISCOtoolkit is a Python package for accessing the data and tools of the [DISCO database](https://disco.bii.a-star.edu.sg/) (DISCO v1). Read the documentation, with tutorials and the API reference, at [disco.bii.a-star.edu.sg/v1/docs/toolkit/guide](https://disco.bii.a-star.edu.sg/v1/docs/toolkit/guide/).
 
@@ -52,7 +52,7 @@ DISCOtoolkit is a Python package for accessing the data and tools of the [DISCO
 - CELLiD: cell type annotation
 - scEnrichment: gene set enrichment using DISCO DEGs
 
-> **DISCO v1 and v2.** The toolkit talks to **DISCO v1** by default. DISCO v2 has its own R package ([DISCOtoolkit](https://github.com/JinmiaoChenLab/DISCOtoolkit)); the Python package can still be pointed at a v2 server, see [Choosing a server](#choosing-a-server).
+> **Use DISCO v1.** The toolkit is developed and tested against **DISCO v1**, which is the default, and that is the server we recommend. DISCO v2 has its own R package ([DISCOtoolkit](https://github.com/JinmiaoChenLab/DISCOtoolkit)). The Python package can be pointed at a v2 server, but that is not tested; see [Choosing a server](#choosing-a-server).
 
 ## Quickstart (Google Colab)
 
@@ -102,7 +102,7 @@ python -m pip install -U discotoolkit
 import discotoolkit as dt
 
 dt.get_server()                       # 'https://disco.bii.a-star.edu.sg/disco_v3_api/'  (DISCO v1, the default)
-dt.set_server("v2")                   # DISCO v2
+dt.set_server("v2")                   # DISCO v2 (not tested; DISCO v1 is the supported server)
 dt.set_server("https://my.server/disco_v3_api/")   # any server with the same API
 ```
 
@@ -117,7 +117,7 @@ python tests/test_settings.py           # offline: server selection logic
 python tests/test_version.py            # offline: setup.py and __init__.py agree on the version
 python tests/test_docs.py               # offline: notebooks are clean, every public function is in the API reference
 python tests/test_server_contract.py    # online: does the server answer everything the toolkit needs?
-python tests/test_server_contract.py https://immunesinglecell.org/disco_v3_api/   # check another server
+python tests/test_server_contract.py <api root>   # check another server
 ```
 
 GitHub Actions runs these, and installs the package on Python 3.9-3.12, on every push. Maintainers: see [RELEASING.md](RELEASING.md) for how a release, and its documentation, is published.

{discotoolkit-1.2.1 → discotoolkit-1.2.2}/README.md

@@ -8,7 +8,7 @@
 -->
 [![Documentation](https://img.shields.io/badge/docs-disco.bii.a--star.edu.sg-blue)](https://disco.bii.a-star.edu.sg/v1/docs/toolkit/guide/) [![Downloads](https://static.pepy.tech/personalized-badge/discotoolkit?period=total&units=international_system&left_color=black&right_color=orange&left_text=Downloads)](https://pepy.tech/project/discotoolkit) [![PyPI version](https://img.shields.io/pypi/v/discotoolkit)](https://pypi.org/project/discotoolkit)
 
-# DISCOtoolkit 1.2.1
+# DISCOtoolkit 1.2.2
 
 DISCOtoolkit is a Python package for accessing the data and tools of the [DISCO database](https://disco.bii.a-star.edu.sg/) (DISCO v1). Read the documentation, with tutorials and the API reference, at [disco.bii.a-star.edu.sg/v1/docs/toolkit/guide](https://disco.bii.a-star.edu.sg/v1/docs/toolkit/guide/).
 
@@ -17,7 +17,7 @@ DISCOtoolkit is a Python package for accessing the data and tools of the [DISCO
 - CELLiD: cell type annotation
 - scEnrichment: gene set enrichment using DISCO DEGs
 
-> **DISCO v1 and v2.** The toolkit talks to **DISCO v1** by default. DISCO v2 has its own R package ([DISCOtoolkit](https://github.com/JinmiaoChenLab/DISCOtoolkit)); the Python package can still be pointed at a v2 server, see [Choosing a server](#choosing-a-server).
+> **Use DISCO v1.** The toolkit is developed and tested against **DISCO v1**, which is the default, and that is the server we recommend. DISCO v2 has its own R package ([DISCOtoolkit](https://github.com/JinmiaoChenLab/DISCOtoolkit)). The Python package can be pointed at a v2 server, but that is not tested; see [Choosing a server](#choosing-a-server).
 
 ## Quickstart (Google Colab)
 
@@ -67,7 +67,7 @@ python -m pip install -U discotoolkit
 import discotoolkit as dt
 
 dt.get_server()                       # 'https://disco.bii.a-star.edu.sg/disco_v3_api/'  (DISCO v1, the default)
-dt.set_server("v2")                   # DISCO v2
+dt.set_server("v2")                   # DISCO v2 (not tested; DISCO v1 is the supported server)
 dt.set_server("https://my.server/disco_v3_api/")   # any server with the same API
 ```
 
@@ -82,7 +82,7 @@ python tests/test_settings.py           # offline: server selection logic
 python tests/test_version.py            # offline: setup.py and __init__.py agree on the version
 python tests/test_docs.py               # offline: notebooks are clean, every public function is in the API reference
 python tests/test_server_contract.py    # online: does the server answer everything the toolkit needs?
-python tests/test_server_contract.py https://immunesinglecell.org/disco_v3_api/   # check another server
+python tests/test_server_contract.py <api root>   # check another server
 ```
 
 GitHub Actions runs these, and installs the package on Python 3.9-3.12, on every push. Maintainers: see [RELEASING.md](RELEASING.md) for how a release, and its documentation, is published.

{discotoolkit-1.2.1 → discotoolkit-1.2.2}/discotoolkit/GlobalVariable.py

@@ -2,8 +2,9 @@
 Settings shared by the rest of the package: logging, the request timeout and --
 most importantly -- which DISCO server the toolkit talks to.
 
-By default the toolkit talks to DISCO v1 (https://disco.bii.a-star.edu.sg). To use
-another server:
+By default the toolkit talks to DISCO v1 (https://disco.bii.a-star.edu.sg). DISCO v1 is the
+server the toolkit is developed and tested against, and the one we recommend. Other servers
+are possible but untested (the "v2" preset in particular):
 
     import discotoolkit as dt
     dt.set_server("v2")                          # a named preset

{discotoolkit-1.2.1 → discotoolkit-1.2.2}/discotoolkit/__init__.py

@@ -5,4 +5,4 @@ from .CELLiD import *
 from .GeneSearch import *
 from .GlobalVariable import set_server, get_server
 
-__version__ = "1.2.1"
+__version__ = "1.2.2"

{discotoolkit-1.2.1 → discotoolkit-1.2.2}/discotoolkit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: discotoolkit
-Version: 1.2.1
+Version: 1.2.2
 Summary: DISCOtoolkit is an python package that allows users to access data and use the tools provided by the DISCO database.
 Home-page: https://disco.bii.a-star.edu.sg/
 Author: Li Mengwei, Rom Uddamvathanak
@@ -43,7 +43,7 @@ Dynamic: summary
 -->
 [![Documentation](https://img.shields.io/badge/docs-disco.bii.a--star.edu.sg-blue)](https://disco.bii.a-star.edu.sg/v1/docs/toolkit/guide/) [![Downloads](https://static.pepy.tech/personalized-badge/discotoolkit?period=total&units=international_system&left_color=black&right_color=orange&left_text=Downloads)](https://pepy.tech/project/discotoolkit) [![PyPI version](https://img.shields.io/pypi/v/discotoolkit)](https://pypi.org/project/discotoolkit)
 
-# DISCOtoolkit 1.2.1
+# DISCOtoolkit 1.2.2
 
 DISCOtoolkit is a Python package for accessing the data and tools of the [DISCO database](https://disco.bii.a-star.edu.sg/) (DISCO v1). Read the documentation, with tutorials and the API reference, at [disco.bii.a-star.edu.sg/v1/docs/toolkit/guide](https://disco.bii.a-star.edu.sg/v1/docs/toolkit/guide/).
 
@@ -52,7 +52,7 @@ DISCOtoolkit is a Python package for accessing the data and tools of the [DISCO
 - CELLiD: cell type annotation
 - scEnrichment: gene set enrichment using DISCO DEGs
 
-> **DISCO v1 and v2.** The toolkit talks to **DISCO v1** by default. DISCO v2 has its own R package ([DISCOtoolkit](https://github.com/JinmiaoChenLab/DISCOtoolkit)); the Python package can still be pointed at a v2 server, see [Choosing a server](#choosing-a-server).
+> **Use DISCO v1.** The toolkit is developed and tested against **DISCO v1**, which is the default, and that is the server we recommend. DISCO v2 has its own R package ([DISCOtoolkit](https://github.com/JinmiaoChenLab/DISCOtoolkit)). The Python package can be pointed at a v2 server, but that is not tested; see [Choosing a server](#choosing-a-server).
 
 ## Quickstart (Google Colab)
 
@@ -102,7 +102,7 @@ python -m pip install -U discotoolkit
 import discotoolkit as dt
 
 dt.get_server()                       # 'https://disco.bii.a-star.edu.sg/disco_v3_api/'  (DISCO v1, the default)
-dt.set_server("v2")                   # DISCO v2
+dt.set_server("v2")                   # DISCO v2 (not tested; DISCO v1 is the supported server)
 dt.set_server("https://my.server/disco_v3_api/")   # any server with the same API
 ```
 
@@ -117,7 +117,7 @@ python tests/test_settings.py           # offline: server selection logic
 python tests/test_version.py            # offline: setup.py and __init__.py agree on the version
 python tests/test_docs.py               # offline: notebooks are clean, every public function is in the API reference
 python tests/test_server_contract.py    # online: does the server answer everything the toolkit needs?
-python tests/test_server_contract.py https://immunesinglecell.org/disco_v3_api/   # check another server
+python tests/test_server_contract.py <api root>   # check another server
 ```
 
 GitHub Actions runs these, and installs the package on Python 3.9-3.12, on every push. Maintainers: see [RELEASING.md](RELEASING.md) for how a release, and its documentation, is published.

{discotoolkit-1.2.1 → discotoolkit-1.2.2}/setup.py

@@ -6,7 +6,7 @@ with open("requirements.txt", "r") as f:
 
 setup(
     name='discotoolkit',
-    version="1.2.1",
+    version="1.2.2",
     url='https://disco.bii.a-star.edu.sg/',
     author='Li Mengwei, Rom Uddamvathanak',
     author_email='uddamvathanak_rom@immunol.a-star.edu.sg',

{discotoolkit-1.2.1 → discotoolkit-1.2.2}/tests/test_docs.py

@@ -72,6 +72,28 @@ def test_api_reference_names_only_things_that_exist():
         assert re.search(r"^(def|class)\s+%s\b" % name, source, re.M), "%s.%s is gone" % (module, name)
 
 
+def test_tutorials_link_to_pages_not_to_notebook_files_and_not_to_the_v2_site():
+    problems = []
+    for path in sorted(glob.glob(os.path.join(ROOT, "docs", "*.ipynb"))):
+        text = "\n".join("".join(c["source"]) for c in json.load(open(path, encoding="utf-8"))["cells"])
+        name = os.path.basename(path)
+        # a relative link to another .ipynb works on GitHub but is a dead link on the site
+        for target in re.findall(r"\]\(([^)\s]+)\)", text):
+            if target.endswith(".ipynb") and not target.startswith("http"):
+                problems.append("%s links to the file %s; link to the page on the docs site" % (name, target))
+        if "immunesinglecell.org" in text:
+            problems.append("%s sends readers to the DISCO V2 site; V1 is the supported server" % name)
+    assert not problems, "; ".join(problems)
+
+
+def test_the_changelog_has_notes_for_the_current_version():
+    # the release workflow builds the GitHub Release text from it, and refuses a version without notes
+    version = re.search(r'__version__\s*=\s*"([^"]+)"', read("discotoolkit/__init__.py")).group(1)
+    assert re.search(r"^## %s\b" % re.escape(version), read("CHANGELOG.md"), re.M), (
+        "add a '## %s' section to CHANGELOG.md before releasing" % version
+    )
+
+
 def _run_all():
     tests = [(n, f) for n, f in sorted(globals().items()) if n.startswith("test_") and callable(f)]
     failed = 0

{discotoolkit-1.2.1 → discotoolkit-1.2.2}/tests/test_server_contract.py

@@ -5,7 +5,7 @@ Needs only `requests`, so it runs anywhere -- including a fresh Colab notebook:
 
     !pip install requests
     !python tests/test_server_contract.py                                # DISCO v1 (default)
-    !python tests/test_server_contract.py https://immunesinglecell.org/disco_v3_api/   # another server
+    !python tests/test_server_contract.py <api root>                                   # another server
 
 or with pytest:  DISCO_API_URL=<api root> pytest tests/test_server_contract.py