datalab-api 0.2.1__tar.gz → 0.2.4__tar.gz

{datalab_api-0.2.1/src/datalab_api.egg-info → datalab_api-0.2.4}/PKG-INFO

@@ -1,8 +1,13 @@
 Metadata-Version: 2.1
 Name: datalab-api
-Version: 0.2.1
+Version: 0.2.4
+Summary: A Python API for instances of the datalab data management platform (https://github.com/the-grey-group/datalab).
 Author-email: Matthew Evans <matthew@ml-evs.science>
 License: MIT
+Project-URL: homepage, https://github.com/datalab-org/datalab-api
+Project-URL: repository, https://github.com/datalab-org/datalab-api
+Project-URL: documentation, https://datalab-python-api.readthedocs.io
+Project-URL: changelog, https://github.com/datalab-org/datalab-api/releases
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3
@@ -21,6 +26,9 @@ Requires-Dist: bokeh~=2.4
 Requires-Dist: rich~=13.0
 Provides-Extra: dev
 Requires-Dist: pre-commit~=3.0; extra == "dev"
+Requires-Dist: pytest~=8.0; extra == "dev"
+Requires-Dist: pytest-cov~=5.0; extra == "dev"
+Requires-Dist: respx~=0.21; extra == "dev"
 Provides-Extra: docs
 Requires-Dist: mkdocs; extra == "docs"
 Requires-Dist: mkdocs-material; extra == "docs"
@@ -30,6 +38,11 @@ Requires-Dist: mkdocs-jupyter; extra == "docs"
 Provides-Extra: cli
 Requires-Dist: typer~=0.9; extra == "cli"
 Requires-Dist: click-shell~=2.1; extra == "cli"
+Provides-Extra: cheminventory-helper
+Requires-Dist: pandas~=2.2; extra == "cheminventory-helper"
+Requires-Dist: openpyxl~=3.0; extra == "cheminventory-helper"
+Provides-Extra: all
+Requires-Dist: datalab-api[cli,dev,docs]; extra == "all"
 
 # <div align="center"><i>datalab</i> Python API</div>
 
@@ -95,7 +108,7 @@ This package implements basic functionality for displaying and manipulating entr
 ```python
 from datalab_api import DatalabClient
 
-with DatalabClient("https://api.public.odbx.science") as client:
+with DatalabClient("https://public.api.odbx.science") as client:
 
     # List all items of a given type
     items = client.get_items()

{datalab_api-0.2.1 → datalab_api-0.2.4}/README.md

@@ -62,7 +62,7 @@ This package implements basic functionality for displaying and manipulating entr
 ```python
 from datalab_api import DatalabClient
 
-with DatalabClient("https://api.public.odbx.science") as client:
+with DatalabClient("https://public.api.odbx.science") as client:
 
     # List all items of a given type
     items = client.get_items()

datalab_api-0.2.4/pyproject.toml

@@ -0,0 +1,175 @@
+[build-system]
+requires = ["setuptools >= 62", "versioningit ~= 3.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "datalab-api"
+readme = "README.md"
+description = "A Python API for instances of the datalab data management platform (https://github.com/the-grey-group/datalab)."
+keywords = []
+license = { text = "MIT" }
+authors = [{ name = "Matthew Evans", email = "matthew@ml-evs.science" }]
+dynamic = ["version"]
+classifiers = [
+    "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Information Technology",
+    "Topic :: Other/Nonlisted Topic",
+    "Topic :: Scientific/Engineering",
+]
+
+requires-python = ">=3.9"
+dependencies =[
+    "httpx ~= 0.27", # better HTTP requests
+    "bokeh ~= 2.4",  # interactive plots from datalab directly
+    "rich ~= 13.0",  # nicer terminal output
+]
+
+
+[project.optional-dependencies]
+dev = [
+    "pre-commit ~= 3.0",
+    "pytest ~= 8.0",
+    "pytest-cov ~= 5.0",
+    "respx ~= 0.21",
+]
+
+docs = [
+    "mkdocs",
+    "mkdocs-material",
+    "mkdocstrings[python-legacy]",
+    "mkdocs-awesome-pages-plugin",
+    "mkdocs-jupyter",
+]
+
+cli = [
+    "typer ~= 0.9",   # command line interface
+    "click-shell ~= 2.1", # REPL-like interface
+]
+
+cheminventory-helper = [
+    "pandas ~= 2.2",
+    "openpyxl ~= 3.0"
+]
+
+all = [
+    "datalab-api[dev,docs,cli]"
+]
+
+[project.scripts]
+datalab = "datalab_api.cli:app"
+
+[project.urls]
+homepage = "https://github.com/datalab-org/datalab-api"
+repository = "https://github.com/datalab-org/datalab-api"
+documentation = "https://datalab-python-api.readthedocs.io"
+changelog = "https://github.com/datalab-org/datalab-api/releases"
+
+[tool.versioningit.vcs]
+method = "git"
+default-tag = "0.0.1"
+
+
+[tool.mypy]
+# plugins = "pydantic.mypy"
+ignore_missing_imports = true
+follow_imports = "skip"
+
+[tool.ruff]
+line-length = 100
+target-version = "py39"
+
+[tool.ruff.lint]
+select = ["ALL"]
+ignore = [
+    "A001",
+    "A002",
+    "ANN",     # TODO fix all ANN errors
+    "ARG",     # TODO fix unused method argument
+    "B007",
+    "B028",
+    "B904",
+    "BLE001",
+    "C408",    # Unnecessary (dict/list/tuple) call - remove call
+    "C416",
+    "C419",
+    "C901",    # function too complex
+    "COM812",  # trailing comma missing
+    "D",
+    "D205",
+    "DTZ",     # datetime-tz-now
+    "E501",    # TODO fix line too long
+    "EM",      # exception message must not use f-string literal
+    "ERA001",  # found commented out code
+    "FA100",   # TODO fix FA errors
+    "FBT001",
+    "FBT002",
+    "FBT003",
+    "FIX002",
+    "G004",    # logging uses fstring
+    "G201",
+    "INP001",
+    "ISC001",
+    "N802",    # TODO maybe fix these
+    "N805",
+    "N818",
+    "PD011",   # pandas-use-of-dot-values
+    "PERF102",
+    "PERF203", # try-except-in-loop
+    "PERF401",
+    "PGH003",
+    "PGH004",
+    "PLR",     # pylint-refactor
+    "PLW0602",
+    "PLW0603",
+    "PLW2901",
+    "PT003",
+    "PT004",   # pytest-missing-fixture-name-underscore
+    "PT006",   # pytest-parametrize-names-wrong-type
+    "PT013",   # pytest-incorrect-pytest-import
+    "PTH",     # prefer Pathlib to os.path
+    "PYI024",
+    "RET",
+    "RET504",
+    "RUF005",
+    "RUF012",
+    "RUF013",  # implicit-optional
+    "RUF015",
+    "S106",
+    "S110",
+    "S112",
+    "S311",
+    "S324",    # use of insecure hash function
+    "S507",    # paramiko auto trust
+    "S602",
+    "S603",
+    "S607",
+    "SIM102",
+    "SIM105",
+    "SIM108",
+    "SIM117",
+    "SLF",     # private member accessed outside class
+    "SLOT000",
+    "T201",
+    "TCH",
+    "TD",      # TODOs
+    "TRY",     # long message outside exception class
+    "UP031",
+]
+pydocstyle.convention = "numpy"
+isort.known-first-party = ["jobflow_remote"]
+isort.split-on-trailing-comma = false
+fixable = ["A", "B", "C", "D", "E", "F", "I"]
+unfixable = []
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["F401"]
+"**/tests/*" = ["INP001", "S101"]

{datalab_api-0.2.1 → datalab_api-0.2.4}/src/datalab_api/__init__.py

@@ -1,3 +1,5 @@
+import warnings
+from collections.abc import Iterable
 from pathlib import Path
 from typing import Any, Optional, Union
 
@@ -6,6 +8,10 @@ from ._base import BaseDatalabClient, __version__
 __all__ = ("__version__", "DatalabClient")
 
 
+class DuplicateItemError(ValueError):
+    """Raised when the API operation would create a duplicate item."""
+
+
 class DatalabClient(BaseDatalabClient):
     """A client for the Datalab API.
 
@@ -65,7 +71,7 @@ class DatalabClient(BaseDatalabClient):
         return items[item_type]
 
     def search_items(
-        self, query: str, item_types: Union[list[str], str] = ["samples", "cells"]
+        self, query: str, item_types: Union[Iterable[str], str] = ("samples", "cells")
     ) -> list[dict[str, Any]]:
         """Search for items of the given types that match the query.
 
@@ -95,7 +101,11 @@ class DatalabClient(BaseDatalabClient):
         return items["items"]
 
     def create_item(
-        self, item_id: str, item_type: str, item_data: Optional[dict[str, Any]] = None
+        self,
+        item_id: str,
+        item_type: str,
+        item_data: Optional[dict[str, Any]] = None,
+        collection_id: Optional[str] = None,
     ) -> dict[str, Any]:
         """Create an item with a given ID and item data.
 
@@ -103,12 +113,22 @@ class DatalabClient(BaseDatalabClient):
             item_id: The ID of the item to create.
             item_type: The type of item to create, e.g., 'samples', 'cells'.
             item_data: The data for the item.
+            collection_id: The ID of the collection to add the item to (optional).
+                If such a collection does not exist, one will be made.
 
         """
         new_item = {}
         if item_data is not None:
             new_item = item_data
-        new_item.update(**{"item_id": item_id, "type": item_type})
+        new_item.update({"item_id": item_id, "type": item_type})
+
+        if collection_id is not None:
+            try:
+                collection_immutable_id = self.get_collection(collection_id)["immutable_id"]
+            except RuntimeError:
+                collection_immutable_id = self.create_collection(collection_id)["immutable_id"]
+            new_item["collections"] = new_item.get("collections", [])
+            new_item["collections"].append({"immutable_id": collection_immutable_id})
 
         create_item_url = f"{self.datalab_api_url}/new-sample/"
         create_item_resp = self.session.post(
@@ -118,16 +138,18 @@ class DatalabClient(BaseDatalabClient):
         )
         try:
             created_item = create_item_resp.json()
-            if created_item["status"] != "success":
-                raise RuntimeError(
-                    f"Failed to create item at {create_item_url}: {created_item['status']!r}."
+            if create_item_resp.status_code == 409:
+                raise DuplicateItemError(
+                    f"Item {item_id=} already exists at {create_item_url}: {created_item['status']!r}."
                 )
+            if created_item["status"] != "success":
+                raise RuntimeError(f"Failed to create item at {create_item_url}: {created_item}.")
             return created_item["sample_list_entry"]
 
-        except Exception:
-            raise RuntimeError(
-                f"Failed to create item {item_id=} with data {item_data=} at {create_item_url}: {create_item_resp.status_code=}. Check the item information is correct."
-            )
+        except Exception as exc:
+            raise exc.__class__(
+                f"Failed to create item {item_id=} with data {item_data=} at {create_item_url}: {create_item_resp.status_code=}, {create_item_resp.content}. Check the item information is correct."
+            ) from exc
 
     def update_item(self, item_id: str, item_data: dict[str, Any]) -> dict[str, Any]:
         """Update an item with the given item data.
@@ -214,6 +236,26 @@ class DatalabClient(BaseDatalabClient):
 
         return item["item_data"]
 
+    def get_item_files(self, item_id: str) -> None:
+        """Download all the files for a given item and save them locally
+        in the current working directory.
+
+        Parameters:
+            item_id: The ID of the item to search for.
+
+        """
+
+        item_data = self.get_item(item_id)
+        for f in item_data.get("files", []):
+            file_location = f["location"]
+            url = file_location.replace("/app", self.datalab_api_url)
+            if Path(f["name"]).exists():
+                warnings.warn(f"Will not overwrite existing file {f['name']}")
+                continue
+            with open(f["name"], "wb") as file:
+                response = self.session.get(url, follow_redirects=True)
+                file.write(response.content)
+
     def get_block(self, item_id: str, block_id: str, block_data: dict[str, Any]) -> dict[str, Any]:
         """Get a block with a given ID and block data.
         Should be used in conjunction with `get_item` to load an existing block.
@@ -369,3 +411,57 @@ class DatalabClient(BaseDatalabClient):
             raise RuntimeError(f"Failed to update block {block_type=}:\n{resp.text}")
 
         return resp.json()["new_block_data"]
+
+    def get_collection(self, collection_id: str) -> dict[str, Any]:
+        """Get a collection with a given ID.
+
+        Parameters:
+            collection_id: The ID of the collection to search for.
+
+        Returns:
+            A dictionary of collection data for the collection with the given ID.
+
+        """
+        collection_url = f"{self.datalab_api_url}/collections/{collection_id}"
+        collection_resp = self.session.get(collection_url, follow_redirects=True)
+        if collection_resp.status_code != 200:
+            raise RuntimeError(
+                f"Failed to find collection {collection_id=} at {collection_url}: {collection_resp.status_code=}. Check the collection ID is correct."
+            )
+        collection = collection_resp.json()
+        if collection["status"] != "success":
+            raise RuntimeError(
+                f"Failed to get collection at {collection_url}: {collection['status']!r}."
+            )
+        return collection["data"]
+
+    def create_collection(
+        self, collection_id: str, collection_data: Optional[dict] = None
+    ) -> dict[str, Any]:
+        """Create a collection with a given ID and collection data.
+
+        Parameters:
+            collection_id: The ID of the collection to create.
+            collection_data: The data for the collection.
+
+        """
+        collection_url = f"{self.datalab_api_url}/collections"
+
+        new_collection = {}
+        if collection_data is not None:
+            new_collection = collection_data
+        new_collection.update({"collection_id": collection_id, "type": "collections"})
+
+        collection_resp = self.session.put(
+            collection_url,
+            json={"data": new_collection},
+            follow_redirects=True,
+        )
+
+        if collection_resp.status_code != 201 or collection_resp.json()["status"] != "success":
+            raise RuntimeError(
+                f"Failed to create collection {collection_id=} at {collection_url}: {collection_resp.status_code=}. Check the collection information is correct: {collection_resp.content}"
+            )
+
+        created_collection = collection_resp.json()["data"]
+        return created_collection

{datalab_api-0.2.1 → datalab_api-0.2.4}/src/datalab_api/_base.py

@@ -1,12 +1,16 @@
 import functools
 import logging
 import os
+import re
+import warnings
 from importlib.metadata import version
 from typing import Any, Optional
 
 import httpx
+from rich.console import Console
 from rich.logging import RichHandler
 from rich.pretty import pprint
+from rich.table import Table
 
 __version__ = version("datalab-api")
 
@@ -14,17 +18,46 @@ __all__ = ("__version__", "BaseDatalabClient")
 
 
 def pretty_displayer(method):
+    """A decorator which wraps a method with a 'display' kwarg, which will
+    either pretty print a JSON response, or display a Rich table.
+
+    """
+
     @functools.wraps(method)
     def rich_wrapper(self, *args, **kwargs):
         display = kwargs.pop("display", False)
+        page_limit = kwargs.pop("page_limit", 10)
         result = method(self, *args, **kwargs)
         if display:
-            if isinstance(result, dict) and "blocks_obj" in result:
-                blocks: dict[str, dict] = result["blocks_obj"]
-                for block in blocks.values():
-                    if "bokeh_plot_data" in block:
-                        bokeh_from_json(block)
-            pprint(result, max_length=None, max_string=100, max_depth=3)
+            blocks = None
+            if isinstance(result, dict):
+                if "blocks_obj" in result:
+                    blocks = result["blocks_obj"]
+                elif "blocktype" in result:
+                    blocks = {result["block_id"]: result}
+                    result = None
+                if blocks:
+                    for block in blocks.values():
+                        if "bokeh_plot_data" in block:
+                            bokeh_from_json(block)
+                if result:
+                    pprint(result, max_length=None, max_string=100, max_depth=3)
+            elif isinstance(result, list):
+                table = Table(show_lines=True)
+                table.add_column("type", overflow="crop", justify="center")
+                table.add_column("ID", style="cyan", no_wrap=True)
+                table.add_column("refcode", style="magenta", no_wrap=True)
+                table.add_column("name", width=30, overflow="ellipsis", no_wrap=True)
+                for item in result[:page_limit]:
+                    table.add_row(
+                        item["type"][0].upper(),
+                        item["item_id"],
+                        item["refcode"],
+                        item["name"],
+                        end_section=True,
+                    )
+                console = Console()
+                console.print(table)
 
         return result
 
@@ -39,16 +72,16 @@ class AutoPrettyPrint(type):
         return super().__new__(cls, name, bases, dct)
 
 
-def bokeh_from_json(block_data):
+def bokeh_from_json(block_data, show=True):
     from bokeh.io import curdoc
-    from bokeh.plotting import show
+    from bokeh.plotting import show as bokeh_show
 
-    if "bokeh_plot_data" in block_data:
-        bokeh_plot_data = block_data["bokeh_plot_data"]
-    else:
-        bokeh_plot_data = block_data
+    bokeh_plot_data = block_data.get("bokeh_plot_data", block_data)
     curdoc().replace_with_json(bokeh_plot_data["doc"])
-    show(curdoc().roots[0])
+    if show:
+        bokeh_show(curdoc().roots[0])
+
+    return curdoc()
 
 
 class BaseDatalabClient(metaclass=AutoPrettyPrint):
@@ -98,6 +131,8 @@ class BaseDatalabClient(metaclass=AutoPrettyPrint):
         self._http_client = httpx.Client
         self._headers["User-Agent"] = f"Datalab Python API/{__version__}"
 
+        self._detect_api_url()
+
         info_json = self.get_info()
 
         self._datalab_api_versions: list[str] = info_json["data"]["attributes"][
@@ -110,6 +145,27 @@ class BaseDatalabClient(metaclass=AutoPrettyPrint):
 
         self._find_api_key()
 
+    def _detect_api_url(self) -> None:
+        """Perform a handshake with the chosen URL to ascertain the correct API URL.
+
+        If a datalab UI URL is passed, the client will attempt to resolve the API URL by
+        inspecting the HTML meta tags.
+
+        Do not use the session for this, so we are not passing the API key to arbitrary URLs.
+
+        """
+        response = httpx.get(self.datalab_api_url)
+        match = re.search(
+            r'<meta name="x_datalab_api_url" content="(.*?)">',
+            response.text,
+            re.IGNORECASE,
+        )
+        if match:
+            self.datalab_api_url = match.group(1)
+            warnings.warn(
+                f"Found API URL {self.datalab_api_url} in HTML meta tag. Creating client with this URL instead."
+            )
+
     def get_info(self) -> dict[str, Any]:
         raise NotImplementedError
 

datalab_api-0.2.4/src/datalab_api/helpers.py

@@ -0,0 +1,51 @@
+import random
+from pathlib import Path
+
+from datalab_api import DatalabClient, DuplicateItemError
+
+
+def import_cheminventory(filename: Path, client: DatalabClient):
+    """Helper function to import a ChemInventory xlsx export into datalab, using the
+    'starting_materials' item type.
+
+    Migrated from the original version in the main datalab repository:
+        https://github.com/the-grey-group/datalab/blob/43764fb494c2cc1bf9f7dc90c25594aeb79d5767/pydatalab/tasks.py#L350-L413
+
+    """
+
+    def _generate_random_startingmaterial_id():
+        """Generate 'XX' + a random 15-length string for use as an id for starting materials
+        that don't have a barcode.
+        """
+        yield "".join(["XX"] + random.choices("abcdefghijklmnopqrstuvwxyz0123456789", k=15))
+
+    try:
+        import pandas as pd
+
+        inventory_df = pd.read_excel(filename)
+    except ImportError as exc:
+        raise ImportError(
+            "Please install pandas + openpyxl to use this helper function, via `pip install datalab-api[cheminventory-helper]`"
+        ) from exc
+    inventory_df["type"] = "starting_materials"
+    inventory_df["item_id"] = inventory_df["Barcode"]
+    # Fill missing barcodes
+    inventory_df["item_id"] = inventory_df["item_id"].fillna(
+        inventory_df["item_id"].apply(lambda _: _generate_random_startingmaterial_id())
+    )
+    inventory_df["Molecular Weight"] = inventory_df["Molecular Weight"].replace(" ", float("nan"))
+
+    inventory_df = inventory_df.dropna()
+
+    counts = {"success": 0, "duplicate": 0}
+
+    for item in inventory_df.to_dict(orient="records"):
+        try:
+            client.create_item(
+                item["item_id"], item["type"], item, collection_id="jul24-inventory-import"
+            )
+            counts["success"] += 1
+        except DuplicateItemError:
+            counts["duplicate"] += 1
+
+    print(f"Done: {counts=}")

{datalab_api-0.2.1 → datalab_api-0.2.4/src/datalab_api.egg-info}/PKG-INFO

@@ -1,8 +1,13 @@
 Metadata-Version: 2.1
 Name: datalab-api
-Version: 0.2.1
+Version: 0.2.4
+Summary: A Python API for instances of the datalab data management platform (https://github.com/the-grey-group/datalab).
 Author-email: Matthew Evans <matthew@ml-evs.science>
 License: MIT
+Project-URL: homepage, https://github.com/datalab-org/datalab-api
+Project-URL: repository, https://github.com/datalab-org/datalab-api
+Project-URL: documentation, https://datalab-python-api.readthedocs.io
+Project-URL: changelog, https://github.com/datalab-org/datalab-api/releases
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3
@@ -21,6 +26,9 @@ Requires-Dist: bokeh~=2.4
 Requires-Dist: rich~=13.0
 Provides-Extra: dev
 Requires-Dist: pre-commit~=3.0; extra == "dev"
+Requires-Dist: pytest~=8.0; extra == "dev"
+Requires-Dist: pytest-cov~=5.0; extra == "dev"
+Requires-Dist: respx~=0.21; extra == "dev"
 Provides-Extra: docs
 Requires-Dist: mkdocs; extra == "docs"
 Requires-Dist: mkdocs-material; extra == "docs"
@@ -30,6 +38,11 @@ Requires-Dist: mkdocs-jupyter; extra == "docs"
 Provides-Extra: cli
 Requires-Dist: typer~=0.9; extra == "cli"
 Requires-Dist: click-shell~=2.1; extra == "cli"
+Provides-Extra: cheminventory-helper
+Requires-Dist: pandas~=2.2; extra == "cheminventory-helper"
+Requires-Dist: openpyxl~=3.0; extra == "cheminventory-helper"
+Provides-Extra: all
+Requires-Dist: datalab-api[cli,dev,docs]; extra == "all"
 
 # <div align="center"><i>datalab</i> Python API</div>
 
@@ -95,7 +108,7 @@ This package implements basic functionality for displaying and manipulating entr
 ```python
 from datalab_api import DatalabClient
 
-with DatalabClient("https://api.public.odbx.science") as client:
+with DatalabClient("https://public.api.odbx.science") as client:
 
     # List all items of a given type
     items = client.get_items()

{datalab_api-0.2.1 → datalab_api-0.2.4}/src/datalab_api.egg-info/SOURCES.txt

@@ -4,9 +4,11 @@ pyproject.toml
 src/datalab_api/__init__.py
 src/datalab_api/_base.py
 src/datalab_api/cli.py
+src/datalab_api/helpers.py
 src/datalab_api.egg-info/PKG-INFO
 src/datalab_api.egg-info/SOURCES.txt
 src/datalab_api.egg-info/dependency_links.txt
 src/datalab_api.egg-info/entry_points.txt
 src/datalab_api.egg-info/requires.txt
-src/datalab_api.egg-info/top_level.txt
+src/datalab_api.egg-info/top_level.txt
+tests/test_client.py

{datalab_api-0.2.1 → datalab_api-0.2.4}/src/datalab_api.egg-info/requires.txt

@@ -2,12 +2,22 @@ httpx~=0.27
 bokeh~=2.4
 rich~=13.0
 
+[all]
+datalab-api[cli,dev,docs]
+
+[cheminventory-helper]
+pandas~=2.2
+openpyxl~=3.0
+
 [cli]
 typer~=0.9
 click-shell~=2.1
 
 [dev]
 pre-commit~=3.0
+pytest~=8.0
+pytest-cov~=5.0
+respx~=0.21
 
 [docs]
 mkdocs

datalab_api-0.2.4/tests/test_client.py

@@ -0,0 +1,22 @@
+import pytest
+import respx
+from datalab_api import DatalabClient
+from httpx import Response
+
+
+@respx.mock
+def test_redirect_url(fake_ui_html, fake_info_json):
+    fake_ui = respx.get("https://ui.datalab.industries").mock(
+        return_value=Response(200, content=fake_ui_html)
+    )
+    fake_api = respx.get("https://api.datalab.industries/info").mock(
+        return_value=Response(200, json=fake_info_json)
+    )
+    with pytest.warns(
+        UserWarning,
+        match="^Found API URL https://api.datalab.industries in HTML meta tag. Creating client with this URL instead.$",
+    ):
+        client = DatalabClient("https://ui.datalab.industries")
+    assert fake_ui.called
+    assert fake_api.called
+    assert client.datalab_api_url == "https://api.datalab.industries"

datalab_api-0.2.1/pyproject.toml

@@ -1,79 +0,0 @@
-[build-system]
-requires = ["setuptools >= 62", "versioningit ~= 3.0", "wheel"]
-build-backend = "setuptools.build_meta"
-
-[project]
-name = "datalab-api"
-readme = "README.md"
-keywords = []
-license = { text = "MIT" }
-authors = [{ name = "Matthew Evans", email = "matthew@ml-evs.science" }]
-dynamic = ["version"]
-classifiers = [
-    "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
-    "Intended Audience :: Science/Research",
-    "Intended Audience :: Information Technology",
-    "Topic :: Other/Nonlisted Topic",
-    "Topic :: Scientific/Engineering",
-]
-
-requires-python = ">=3.9"
-dependencies =[
-    "httpx ~= 0.27", # better HTTP requests
-    "bokeh ~= 2.4",  # interactive plots from datalab directly
-    "rich ~= 13.0",  # nicer terminal output
-]
-
-
-[project.optional-dependencies]
-dev = [
-    "pre-commit ~= 3.0",
-]
-
-docs = [
-    "mkdocs",
-    "mkdocs-material",
-    "mkdocstrings[python-legacy]",
-    "mkdocs-awesome-pages-plugin",
-    "mkdocs-jupyter",
-]
-
-cli = [
-    "typer ~= 0.9",   # command line interface
-    "click-shell ~= 2.1", # REPL-like interface
-]
-
-[project.scripts]
-datalab = "datalab_api.cli:app"
-
-[project.urls]
-# homepage = "https://github.com/the-grey-group/datalab"
-# repository = "https://github.com/the-grey-group/datalab"
-# documentation = "https://the-datalab.readthedocs.io"
-# changelog = "https://github.com/the-grey-group/datalab/releases"
-
-[tool.versioningit.vcs]
-method = "git"
-default-tag = "0.0.1"
-
-
-[tool.mypy]
-# plugins = "pydantic.mypy"
-ignore_missing_imports = true
-follow_imports = "skip"
-
-[tool.ruff]
-line-length = 100
-target-version = "py310"
-
-[tool.ruff.lint]
-select = ["E", "F", "I", "W", "Q"]
-ignore = ["E501", "E402"]
-fixable = ["A", "B", "C", "D", "E", "F", "I"]
-unfixable = []
-per-file-ignores = {}
-# Allow unused variables when underscore-prefixed.
-dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"