refscan 0.3.2__tar.gz → 0.3.3__tar.gz

{refscan-0.3.2 → refscan-0.3.3}/PKG-INFO

@@ -1,19 +1,13 @@
 Metadata-Version: 2.3
 Name: refscan
-Version: 0.3.2
+Version: 0.3.3
 Summary: Command-line program that scans the NMDC MongoDB database for referential integrity violations
 Keywords: mongodb,mongo,relationships,reference,database,data,referential integrity,scan
-Requires-Python: >=3.9,<4.0
-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: Programming Language :: Python :: 3.13
-Requires-Dist: linkml-runtime (>=1.7.5,<2.0.0)
-Requires-Dist: pymongo (>=4.7.1,<5.0.0)
-Requires-Dist: rich (>=13.7.1,<14.0.0)
-Requires-Dist: typer (>=0.15.1,<0.16.0)
+Requires-Dist: linkml-runtime>=1.7.5,<2
+Requires-Dist: pymongo>=4.7.1,<5
+Requires-Dist: rich>=13.7.1,<14
+Requires-Dist: typer>=0.15.1,<0.16
+Requires-Python: >=3.9, <3.10
 Project-URL: Documentation, https://github.com/microbiomedata/refscan
 Project-URL: Homepage, https://github.com/microbiomedata/refscan
 Project-URL: Repository, https://github.com/microbiomedata/refscan
@@ -269,10 +263,12 @@ pipx uninstall refscan
 
 ## Development
 
-We use [Poetry](https://python-poetry.org/) to both (a) manage dependencies and (b) build distributable packages that can be published to PyPI.
+We use [`uv`](https://docs.astral.sh/uv/) to both (a) manage dependencies and (b) build distributable packages that can be published to PyPI.
 
-- `pyproject.toml`: Configuration file for Poetry and other tools (was initialized via `$ poetry init`)
-- `poetry.lock`: List of dependencies, both direct and [indirect/transitive](https://en.wikipedia.org/wiki/Transitive_dependency)
+- `pyproject.toml`: [Configuration file](https://packaging.python.org/en/latest/guides/writing-pyproject-toml/) for `uv` and other tools
+- `uv.lock`: List of dependencies, both direct and [indirect/transitive](https://en.wikipedia.org/wiki/Transitive_dependency)
+
+> Note: We initialized this repository using Poetry. We switched from Poetry to `uv` at around commit `#1449ceca`.
 
 ### Clone repository
 
@@ -281,28 +277,29 @@ git clone https://github.com/microbiomedata/refscan.git
 cd refscan
 ```
 
-### Create virtual environment
+### Set up Python virtual environment
 
-Create a Poetry virtual environment and attach to its shell:
+You can set up a Python virtual environment by issuing the following command from the root directory of the repository:
 
 ```shell
-poetry shell
+uv sync
 ```
 
-> You can see information about the Poetry virtual environment by running: `$ poetry env info`
-
-> You can detach from the Poetry virtual environment's shell by running: `$ exit`
+That command will:
+1. **Create a Python virtual environment** at `.venv` (if one doesn't already exist there)
+2. **Install all dependencies** described in `uv.lock` into that Python virtual environment
+3. Uninstall all dependencies _not_ described in `uv.lock` from that Python virtual environment
 
-From now on, I'll refer to the Poetry virtual environment's shell as the "Poetry shell."
+### Activate Python virtual environment
 
-### Install dependencies
-
-At the Poetry shell, install the project's dependencies:
+Now that you have set up a Python virtual environment, you can activate it by issuing the following command:
 
 ```shell
-poetry install
+source .venv/bin/activate
 ```
 
+> Note: Once you're ready to _deactivate_ the Python virtual environment, you can do so by running `$ deactivate`.
+
 ### Make changes
 
 Edit the tool's source code and documentation however you want.
@@ -310,7 +307,7 @@ Edit the tool's source code and documentation however you want.
 While editing the tool's source code, you can run the tool as you normally would in order to test things out.
 
 ```shell
-poetry run refscan --help
+uv run refscan --help
 ```
 
 ### Check types
@@ -320,7 +317,7 @@ We use [mypy](https://mypy.readthedocs.io/en/stable/) as the static type checker
 You can perform static type checking by running the following command from the root directory of the repository:
 
 ```shell
-poetry run mypy
+uv run mypy
 ```
 
 ### Run tests
@@ -332,29 +329,45 @@ Tests are defined in the `tests` directory.
 You can run the tests by running the following command from the root directory of the repository:
 
 ```shell
-poetry run pytest
+uv run pytest
 ```
 
 ### Format code
 
-We use [`black`](https://black.readthedocs.io/en/stable/) as the code formatter for `refscan`. 
+We use [`ruff`](https://docs.astral.sh/ruff/formatter/) as the code _formatter_ for `refscan`.
 
-We do not use it with its default options. Instead, we include an option that allows lines to be 120 characters
-instead of the default 88 characters. That option is defined in the `[tool.black]` section of `pyproject.toml`.
+We mostly use it with its default rules. All of the ways we deviate from those are listed
+in the `[tool.ruff]` section of `pyproject.toml`.
 
-You can format all the Python code in the repository by running this command
-from the root directory of the repository:
+You can _check_ the code's compliance with the "formatter rules" by running this command from the root directory of the repository:
 
 ```shell
-poetry run black .
+uv run ruff format --check
 ```
 
-#### Check format
+That will output a _list_ of files that don't comply. To see the violations, themselves, you can run:
 
-You can _check_ the format of the Python code by including the `--check` option, like this:
+```shell
+uv run ruff format --diff
+```
+
+You can _format_ the code by omitting the `--check` and `--diff` flags:
 
 ```shell
-poetry run black --check .
+uv run ruff format
+```
+
+### Lint code
+
+We also use [`ruff`](https://docs.astral.sh/ruff/linter/) as the code _linter_ for `refscan`.
+
+We use it with its [default rules](https://docs.astral.sh/ruff/rules/), **plus** some additional ones,
+all of which are listed in the `[tool.ruff.lint]` section of `pyproject.toml`.
+
+You can _check_ the code's compliance with the "linter rules" by running this command from the root directory of the repository:
+
+```shell
+uv run ruff check
 ```
 
 ## Building and publishing
@@ -371,7 +384,7 @@ That package will have a version identifier that matches the name of the Git tag
 In case you want to test the build process locally, you can do so by running:
 
 ```shell
-poetry build
+uv build
 ```
 
 > That will create both a
@@ -379,4 +392,3 @@ poetry build
 > file (whose name ends with `.tar.gz`) and a
 > [wheel](https://packaging.python.org/en/latest/specifications/binary-distribution-format/#binary-distribution-format)
 > file (whose name ends with `.whl`) in the `dist` directory.
-

{refscan-0.3.2 → refscan-0.3.3}/README.md

@@ -248,10 +248,12 @@ pipx uninstall refscan
 
 ## Development
 
-We use [Poetry](https://python-poetry.org/) to both (a) manage dependencies and (b) build distributable packages that can be published to PyPI.
+We use [`uv`](https://docs.astral.sh/uv/) to both (a) manage dependencies and (b) build distributable packages that can be published to PyPI.
 
-- `pyproject.toml`: Configuration file for Poetry and other tools (was initialized via `$ poetry init`)
-- `poetry.lock`: List of dependencies, both direct and [indirect/transitive](https://en.wikipedia.org/wiki/Transitive_dependency)
+- `pyproject.toml`: [Configuration file](https://packaging.python.org/en/latest/guides/writing-pyproject-toml/) for `uv` and other tools
+- `uv.lock`: List of dependencies, both direct and [indirect/transitive](https://en.wikipedia.org/wiki/Transitive_dependency)
+
+> Note: We initialized this repository using Poetry. We switched from Poetry to `uv` at around commit `#1449ceca`.
 
 ### Clone repository
 
@@ -260,28 +262,29 @@ git clone https://github.com/microbiomedata/refscan.git
 cd refscan
 ```
 
-### Create virtual environment
+### Set up Python virtual environment
 
-Create a Poetry virtual environment and attach to its shell:
+You can set up a Python virtual environment by issuing the following command from the root directory of the repository:
 
 ```shell
-poetry shell
+uv sync
 ```
 
-> You can see information about the Poetry virtual environment by running: `$ poetry env info`
-
-> You can detach from the Poetry virtual environment's shell by running: `$ exit`
+That command will:
+1. **Create a Python virtual environment** at `.venv` (if one doesn't already exist there)
+2. **Install all dependencies** described in `uv.lock` into that Python virtual environment
+3. Uninstall all dependencies _not_ described in `uv.lock` from that Python virtual environment
 
-From now on, I'll refer to the Poetry virtual environment's shell as the "Poetry shell."
+### Activate Python virtual environment
 
-### Install dependencies
-
-At the Poetry shell, install the project's dependencies:
+Now that you have set up a Python virtual environment, you can activate it by issuing the following command:
 
 ```shell
-poetry install
+source .venv/bin/activate
 ```
 
+> Note: Once you're ready to _deactivate_ the Python virtual environment, you can do so by running `$ deactivate`.
+
 ### Make changes
 
 Edit the tool's source code and documentation however you want.
@@ -289,7 +292,7 @@ Edit the tool's source code and documentation however you want.
 While editing the tool's source code, you can run the tool as you normally would in order to test things out.
 
 ```shell
-poetry run refscan --help
+uv run refscan --help
 ```
 
 ### Check types
@@ -299,7 +302,7 @@ We use [mypy](https://mypy.readthedocs.io/en/stable/) as the static type checker
 You can perform static type checking by running the following command from the root directory of the repository:
 
 ```shell
-poetry run mypy
+uv run mypy
 ```
 
 ### Run tests
@@ -311,29 +314,45 @@ Tests are defined in the `tests` directory.
 You can run the tests by running the following command from the root directory of the repository:
 
 ```shell
-poetry run pytest
+uv run pytest
 ```
 
 ### Format code
 
-We use [`black`](https://black.readthedocs.io/en/stable/) as the code formatter for `refscan`. 
+We use [`ruff`](https://docs.astral.sh/ruff/formatter/) as the code _formatter_ for `refscan`.
+
+We mostly use it with its default rules. All of the ways we deviate from those are listed
+in the `[tool.ruff]` section of `pyproject.toml`.
+
+You can _check_ the code's compliance with the "formatter rules" by running this command from the root directory of the repository:
+
+```shell
+uv run ruff format --check
+```
 
-We do not use it with its default options. Instead, we include an option that allows lines to be 120 characters
-instead of the default 88 characters. That option is defined in the `[tool.black]` section of `pyproject.toml`.
+That will output a _list_ of files that don't comply. To see the violations, themselves, you can run:
 
-You can format all the Python code in the repository by running this command
-from the root directory of the repository:
+```shell
+uv run ruff format --diff
+```
+
+You can _format_ the code by omitting the `--check` and `--diff` flags:
 
 ```shell
-poetry run black .
+uv run ruff format
 ```
 
-#### Check format
+### Lint code
+
+We also use [`ruff`](https://docs.astral.sh/ruff/linter/) as the code _linter_ for `refscan`.
+
+We use it with its [default rules](https://docs.astral.sh/ruff/rules/), **plus** some additional ones,
+all of which are listed in the `[tool.ruff.lint]` section of `pyproject.toml`.
 
-You can _check_ the format of the Python code by including the `--check` option, like this:
+You can _check_ the code's compliance with the "linter rules" by running this command from the root directory of the repository:
 
 ```shell
-poetry run black --check .
+uv run ruff check
 ```
 
 ## Building and publishing
@@ -350,7 +369,7 @@ That package will have a version identifier that matches the name of the Git tag
 In case you want to test the build process locally, you can do so by running:
 
 ```shell
-poetry build
+uv build
 ```
 
 > That will create both a

refscan-0.3.3/pyproject.toml

@@ -0,0 +1,121 @@
+[project]
+name = "refscan"
+version = "0.3.3"
+description = "Command-line program that scans the NMDC MongoDB database for referential integrity violations"
+authors = []
+# Note: We constrain the Python version to 3.9.* because we know that `nmdc-schema`, which depends upon this
+#       package, is also constrained to Python 3.9.* (according to its `pyproject.toml` file).
+#       Reference: https://github.com/microbiomedata/nmdc-schema/blob/main/pyproject.toml#L34
+requires-python = ">= 3.9, < 3.10"
+readme = "README.md"
+keywords = [
+    "mongodb",
+    "mongo",
+    "relationships",
+    "reference",
+    "database",
+    "data",
+    "referential integrity",
+    "scan",
+]
+dependencies = [
+    # We use `linkml-runtime` to facilitate using `nmdc-schema`.
+    # Docs: https://linkml.io/linkml/developers/schemaview.html#linkml_runtime.utils.schemaview.SchemaView
+    "linkml-runtime >= 1.7.5, < 2",
+    # We use `pymongo` to communicate with MongoDB servers.
+    # Docs: (https://pymongo.readthedocs.io/en/stable/
+    "pymongo >= 4.7.1, < 5",
+    # We use `rich` to format console output.
+    # Docs: https://rich.readthedocs.io/en/stable/index.html
+    "rich >= 13.7.1, < 14",
+    # We use `typer` as a CLI framework.
+    # Docs: https://typer.tiangolo.com/
+    "typer >= 0.15.1, < 0.16",
+]
+
+[project.urls]
+Homepage = "https://github.com/microbiomedata/refscan"
+Repository = "https://github.com/microbiomedata/refscan"
+Documentation = "https://github.com/microbiomedata/refscan"
+
+[project.scripts]
+refscan = "refscan.cli.cli:app"
+
+[dependency-groups]
+dev = [
+    # We use `pyinstrument` for performance profiling.
+    # Usage: $ uv run pyinstrument --from-path refscan --help
+    # Docs: https://pyinstrument.readthedocs.io/en/latest/guide.html#profile-a-python-cli-command
+    "pyinstrument >= 4.6.2, < 5",
+    # We use `pytest` to run tests.
+    # Usage: $ uv run pytest
+    # Docs: https://docs.pytest.org/en/stable/contents.html
+    "pytest >= 8.2.2, < 9",
+    "pytest-cov >= 5.0.0, < 6",
+    # We use `mongomock` to test MongoDB interaction without involving a real MongoDB instance.
+    # Docs: https://github.com/mongomock/mongomock
+    "mongomock >= 4.3.0, < 5",
+    # We use `mypy` to perform static type checking.
+    # Usage: $ uv run mypy
+    # Docs: https://mypy.readthedocs.io/en/stable/
+    "mypy >= 1.16.0, < 2",
+    # We use `ruff` for both code formatting and linting.
+    # Docs: https://docs.astral.sh/ruff/
+    "ruff >= 0.12.11",
+]
+
+[build-system]
+# Note: The `migrate-to-uv` tool (i.e. https://github.com/mkniewallner/migrate-to-uv), which we used to switch
+#       from Poetry to `uv`, set this to use `hatchling`. We then changed it to use `uv_build` instead.
+#       Reference: https://docs.astral.sh/uv/concepts/build-backend/#using-the-uv-build-backend
+requires = ["uv_build >= 0.8.14, < 0.9.0"]
+build-backend = "uv_build"
+
+[tool.uv.build-backend]
+# Note: We specify `module-name` here to tell the `uv_build` backend that our main module is in `refscan/`
+#       (as opposed to being in a `src/` directory, which is where the backend would look for it by default).
+#       Reference: https://docs.astral.sh/uv/concepts/build-backend/#modules
+module-name = "refscan"
+module-root = ""
+
+[tool.pytest.ini_options]
+# Make it so that, when someone runs `$ uv run pytest`, in addition to running the tests, it also (a) runs doctests
+# defined in Python modules, and (b) measures—via the `pytest-cov` plugin—test coverage within the `refscan` folder.
+# Reference (a): https://docs.pytest.org/en/stable/how-to/doctest.html#how-to-run-doctests
+# Reference (b): https://pytest-cov.readthedocs.io/en/latest/config.html#configuration
+addopts = "--doctest-modules --cov=refscan"
+
+[tool.ruff]
+line-length = 120
+
+[tool.ruff.lint]
+# Specify which linting rules will be used when someone runs `$ uv run ruff check`.
+# Note: The default rules are `["E4", "E7", "E9", "F"]`.
+# References:
+# - https://docs.astral.sh/ruff/rules/ (the list of rules)
+# - https://docs.astral.sh/ruff/settings/#lint_select (the `select` setting)
+select = ["E4", "E7", "E9", "F", "D101", "D102", "D103"]
+
+[tool.ruff.lint.per-file-ignores]
+# Ignore some rules when linting files in specified directories.
+# Reference: https://docs.astral.sh/ruff/settings/#lint_per-file-ignores
+"tests/*.py" = ["D101", "D102", "D103"]
+
+[tool.mypy]
+# Make it so, when someone runs `$ uv run mypy`, these default CLI options are used.
+# Reference: https://mypy.readthedocs.io/en/stable/config_file.html
+files = "."
+
+[[tool.mypy.overrides]]
+# Silence the following error:
+# > Skipping analyzing "linkml_runtime": module is installed, but missing library stubs or py.typed marker  [import-untyped] 
+#
+# Note: We first tried using the following, but it seemed to have no effect on the behavior of mypy when run via `$ poetry run mypy` (back when we used poetry instead of uv).
+#       ```
+#       [mypy-linkml_runtime]
+#       ignore_missing_imports = true
+#       ```
+#       So, we—instead—used the syntax shown on: https://stackoverflow.com/a/74198016
+#
+module = "linkml_runtime"
+ignore_missing_imports = true

{refscan-0.3.2 → refscan-0.3.3}/refscan/cli/graph.py

@@ -1,5 +1,4 @@
 from pathlib import Path
-from typing import Optional
 from typing_extensions import Annotated
 
 import typer
@@ -24,7 +23,7 @@ def graph(
         ),
     ],
     graph_file_path: Annotated[
-        Optional[Path],
+        Path,
         typer.Option(
             "--graph",
             dir_okay=False,
@@ -33,7 +32,7 @@ def graph(
             resolve_path=True,
             help="Filesystem path at which you want **refscan** to generate the graph.",
         ),
-    ] = "graph.html",
+    ] = Path("graph.html"),
     subject: Annotated[
         grapher.Subject,
         typer.Option(

{refscan-0.3.2 → refscan-0.3.3}/refscan/cli/scan.py

@@ -71,7 +71,7 @@ def scan(
         ),
     ] = None,
     reference_report_file_path: Annotated[
-        Optional[Path],
+        Path,
         typer.Option(
             "--reference-report",
             dir_okay=False,
@@ -80,9 +80,9 @@ def scan(
             resolve_path=True,
             help="Filesystem path at which you want the program to generate its reference report.",
         ),
-    ] = "references.tsv",
+    ] = Path("references.tsv"),
     violation_report_file_path: Annotated[
-        Optional[Path],
+        Path,
         typer.Option(
             "--violation-report",
             dir_okay=False,
@@ -91,7 +91,7 @@ def scan(
             resolve_path=True,
             help="Filesystem path at which you want the program to generate its violation report.",
         ),
-    ] = "violations.tsv",
+    ] = Path("violations.tsv"),
     user_wants_to_skip_scan: Annotated[
         bool,
         typer.Option(
@@ -202,7 +202,7 @@ def scan(
     num_all_violations = len(all_violations)
     color_name = "white" if num_all_violations == 0 else "red"
     console.print()  # newline
-    console.print(f"Total violations: " f"[{color_name}]{num_all_violations}[/{color_name}]")
+    console.print(f"Total violations: [{color_name}]{num_all_violations}[/{color_name}]")
     console.print()  # newline
 
     # Create a TSV-formatted violation report that lists all violations among all collections.

{refscan-0.3.2 → refscan-0.3.3}/refscan/lib/Finder.py

@@ -63,7 +63,6 @@ class Finder:
         # Check whether either (a) the queue is empty or (b) this collection name is not at the front of the queue.
         # Example: [] is empty, or "b_set" is not the first item in ["a_set", "b_set", "c_set"]
         if len(queue) == 0 or queue[0] != collection_name:
-
             # If this collection name is already (elsewhere) in the queue, remove it from that position, automatically
             # updating the list indexes of subsequent list items (so there is no "gap" in the list).
             # Example: Removing "b_set" from ["a_set", "b_set", "c_set"] → ["a_set", "c_set"]
@@ -86,7 +85,6 @@ class Finder:
 
         # Iterate over the collection names in the queue, from back (oldest) to front (newest).
         for cached_collection_name in reversed(self.cached_collection_names_where_recently_found):
-
             # If this cached collection name is among the eligible ones, move it to the front of the list.
             # Example: Since "b_set" is in ["a_set", "b_set", "c_set"] → ["b_set, "a_set", "c_set"]
             if cached_collection_name in names_of_eligible_collections:
@@ -143,7 +141,6 @@ class Finder:
         # Search the collections.
         query_filter = dict(id=document_id)
         for collection_name in ordered_collection_names:
-
             # Before querying the database, check our cache of document `id` presences/absences per collection.
             is_id_present: Optional[bool] = self._get_cached_id_presence_in_collection(
                 collection_name=collection_name, document_id=document_id

{refscan-0.3.2 → refscan-0.3.3}/refscan/lib/ReferenceList.py

@@ -69,7 +69,6 @@ class ReferenceList(UserList):
         """
         target_collection_names = []
         for reference in self.data:  # note: in a `UserList`, `self.data` refers to the underlying list data structure
-
             # If this reference's source describes the specified source, record the reference's target collection name.
             if reference.source_class_name == source_class_name and reference.source_field_name == source_field_name:
                 target_collection_names.append(reference.target_collection_name)

{refscan-0.3.2 → refscan-0.3.3}/refscan/lib/helpers.py

@@ -241,7 +241,6 @@ def identify_references(
     for collection_name, class_names in sorted_collection_names_to_class_names:
         for class_name in class_names:
             for slot_name in schema_view.class_slots(class_name):
-
                 # Get the slot definition in the context of its use on this particular class.
                 slot_definition = schema_view.induced_slot(slot_name=slot_name, class_name=class_name)
 

{refscan-0.3.2 → refscan-0.3.3}/refscan/scanner.py

@@ -50,7 +50,7 @@ def identify_referring_documents(
     """
 
     # Initialize a list of descriptors of documents that reference the specified document.
-    referring_document_descriptors = []
+    referring_document_descriptors: List[Dict] = []
 
     # If the specified document does not have an `id` field, we know it cannot be referenced.
     if "id" not in document:
@@ -97,7 +97,6 @@ def identify_referring_documents(
 
         # For each referring document, store a descriptor of it.
         for referring_document in referring_documents:
-
             # Handle the case where the source document does not have an `id`.
             #
             # Note: As a reminder, according to the NMDC Schema (as of version v11.8.0), documents in the
@@ -195,7 +194,6 @@ def scan_outgoing_references(
                     )
                 )
                 if name_of_collection_containing_target_document is None:
-
                     # If the user wants to locate misplaced documents,
                     # search all illegal collections for the misplaced document.
                     if user_wants_to_locate_misplaced_documents:
@@ -268,7 +266,6 @@ def scan(
 
     source_collections_and_their_violations: dict[str, ViolationList] = {}
     with custom_progress as progress:
-
         # Filter out the collections that the schema says can contain references, but that don't exist in the database.
         source_collection_names_in_db = []
         for collection_name in references.get_source_collection_names():
@@ -289,7 +286,6 @@ def scan(
         # contain "referrers" (documents), which of their slots can contain references (fields),
         # and which collections can contain the referred-to "referees" (documents).
         for source_collection_name in sorted(source_collection_names_in_db):
-
             # If this source collection is one of the ones the user wanted to skip, skip it now.
             if source_collection_name in names_of_source_collections_to_skip:
                 continue

refscan-0.3.2/LICENSE

@@ -1,42 +0,0 @@
-Refscan Copyright (c) 2024, The Regents of the University of California, 
-through  Lawrence Berkeley National Laboratory (subject to receipt of any 
-required  approvals from the U.S. Dept. of Energy).  All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-(1) Redistributions of source code must retain the above copyright notice,
-this list of conditions and the following disclaimer.
-
-(2) Redistributions in binary form must reproduce the above copyright
-notice, this list of conditions and the following disclaimer in the
-documentation and/or other materials provided with the distribution.
-
-(3) Neither the name of the University of California, Lawrence Berkeley
-National Laboratory, U.S. Dept. of Energy nor the names of its contributors
-may be used to endorse or promote products derived from this software
-without specific prior written permission.
-
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
-LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
-CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
-SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
-CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
-ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-POSSIBILITY OF SUCH DAMAGE.
-
-You are under no obligation whatsoever to provide any bug fixes, patches,
-or upgrades to the features, functionality or performance of the source
-code ("Enhancements") to anyone; however, if you choose to make your
-Enhancements available either publicly, or directly to Lawrence Berkeley
-National Laboratory, without imposing a separate written license agreement
-for such Enhancements, then you hereby grant the following license: a
-non-exclusive, royalty-free perpetual license to install, use, modify,
-prepare derivative works, incorporate into other computer software,
-distribute, and sublicense such enhancements or derivative works thereof,
-in binary and source code form.

refscan-0.3.2/pyproject.toml

@@ -1,89 +0,0 @@
-# Reference: https://python-poetry.org/docs/pyproject/
-
-[tool.poetry]
-name = "refscan"
-version = "v0.3.2"
-description = "Command-line program that scans the NMDC MongoDB database for referential integrity violations"
-authors = []
-readme = "README.md"
-repository = "https://github.com/microbiomedata/refscan"
-homepage = "https://github.com/microbiomedata/refscan"
-documentation = "https://github.com/microbiomedata/refscan"
-keywords = ["mongodb", "mongo", "relationships", "reference", "database", "data", "referential integrity", "scan"]
-
-[tool.poetry.dependencies]
-python = "^3.9"
-# We use `linkml-runtime` to facilitate using `nmdc-schema`.
-# Docs: https://linkml.io/linkml/developers/schemaview.html#linkml_runtime.utils.schemaview.SchemaView
-linkml-runtime = "^1.7.5"
-# We use `pymongo` to communicate with MongoDB servers.
-# Docs: (https://pymongo.readthedocs.io/en/stable/
-pymongo = "^4.7.1"
-# We use `rich` to format console output.
-# Docs: https://rich.readthedocs.io/en/stable/index.html
-rich = "^13.7.1"
-# We use `typer` as a CLI framework.
-# Docs: https://typer.tiangolo.com/
-typer = "^0.15.1"
-
-[tool.poetry.group.dev.dependencies]
-# We use `black` for code formatting.
-# Usage: $ poetry run black --line-length 120 .
-# Docs: https://black.readthedocs.io/en/stable/
-black = "^24.4.2"
-# We use `pyinstrument` for performance profiling.
-# Usage: $ pyinstrument --from-path refscan --help
-# Docs: https://pyinstrument.readthedocs.io/en/latest/guide.html#profile-a-python-cli-command
-pyinstrument = "^4.6.2"
-# We use `pytest` to run tests.
-# Usage: $ poetry run pytest
-# Docs: https://docs.pytest.org/en/stable/contents.html
-pytest = "^8.2.2"
-pytest-cov = "^5.0.0"
-# We use `mongomock` to test MongoDB interaction without involving a real MongoDB instance.
-# Docs: https://github.com/mongomock/mongomock
-mongomock = "^4.3.0"
-# We use `mypy` to perform static type checking.
-# Usage: $ poetry run mypy
-# Docs: https://mypy.readthedocs.io/en/stable/
-mypy = "^1.16.0"
-
-[tool.poetry.scripts]
-# Reference: https://python-poetry.org/docs/pyproject#scripts
-# Reference: https://typer.tiangolo.com/tutorial/package/#add-a-script
-refscan = "refscan.cli.cli:app"
-
-[tool.pytest.ini_options]
-# Make it so that, when someone runs `$ poetry run pytest`, in addition to running the tests, it also (a) runs doctests
-# defined in Python modules, and (b) measures—via the `pytest-cov` plugin—test coverage within the `refscan` folder.
-# Reference (a): https://docs.pytest.org/en/stable/how-to/doctest.html#how-to-run-doctests
-# Reference (b): https://pytest-cov.readthedocs.io/en/latest/config.html#configuration
-addopts = "--doctest-modules --cov=refscan"
-
-[tool.black]
-# Make it so that, when someone runs `$ poetry run black`, these default CLI options are used.
-# Reference: https://black.readthedocs.io/en/stable/usage_and_configuration/the_basics.html#configuration-format
-line-length = 120
-
-[tool.mypy]
-# Make it so, when someone runs `$ poetry run mypy`, these default CLI options are used.
-# Reference: https://mypy.readthedocs.io/en/stable/config_file.html
-files = "."
-
-[[tool.mypy.overrides]]
-# Silence the following error:
-# > Skipping analyzing "linkml_runtime": module is installed, but missing library stubs or py.typed marker  [import-untyped] 
-#
-# Note: We first tried using the following, but it seemed to have no effect on the behavior of mypy when run via `$ poetry run mypy`.
-#       ```
-#       [mypy-linkml_runtime]
-#       ignore_missing_imports = true
-#       ```
-#       So, we—instead—used the syntax shown on: https://stackoverflow.com/a/74198016
-#
-module = "linkml_runtime"
-ignore_missing_imports = true
-
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"