Maint/modernize (#76)

This PR fixes #69.
The aim is to modernize the tooling surrounding `xncml`, including but not limited to:
- migrate from `setup.py` to `pyproject.toml`
- Make use of `ruff` instead of `flake8`, `isort`, `black`, etc.
- Use the src layout as described in https://packaging.python.org/en/latest/discussions/src-layout-vs-flat-layout/

This also adds a `.cruft.json` file coming from the use of [cruft](https://github.com/cruft/cruft) with the [Ouranosinc template](https://github.com/Ouranosinc/cookiecutter-pypackage).
Cruft can then be used to update the project structure whenever the template is updated.
However, the `xncml` project already diverged a little from the original template:
- `CHANGES.rst` is renamed CHANGELOG.rst
- `docs/usage.rst` is superseded by `docs/tutorial.ipynb`
- `ruff` format replaces `black`

# Breaking changes
- Python3.9 has been dropped, Python3.13 support has been added.
- The build system is now using `flit` instead of setuptools.
- setup.py was removed.
- __version__ is no longer fetched from git, but is instead hardcoded in xncml/__init__.py
- All workflows have been replaced
  - Publishing to TestPyPI and PyPI are now handled via Trusted Publishing
  - Testing uses `tox` and reports directly to coveralls.io
  - Many other small changes to aid with maintainability
- Documentation now uses `sphinx-apidoc` to generate an API map that is exposed by ReadTheDocs
- ReadTheDocs builds now fail when the generation step emits any warnings (for ensuring that the documentation is always working as intended)
- `xncml.generated` no longer exposes the `ncml_2_2.py` submodule (needed to prevent multiple targets for the same re-exported functions/modules).

---------

Co-authored-by: Abel Aoun <[email protected]>
Co-authored-by: Francis Charette-Migneault <[email protected]>
Co-authored-by: Zeitsperre <[email protected]>
Co-authored-by: David Huard <[email protected]>

Author: 5 people

.coveragerc

@@ -0,0 +1,31 @@
+{
+  "template": "https://github.com/Ouranosinc/cookiecutter-pypackage.git",
+  "commit": "760bcbb2540bd973d57ea1aa1f1b24759f6d0955",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "full_name": "Abel Aoun",
+      "email": "[email protected]",
+      "github_username": "xarray-contrib",
+      "project_name": "xncml",
+      "project_slug": "xncml",
+      "project_short_description": "Tools for manipulating NcML (NetCDF Markup Language) files with/for xarray",
+      "pypi_username": "bzah",
+      "version": "0.5.0",
+      "use_pytest": "y",
+      "use_black": "n",
+      "use_conda": "n",
+      "add_pyup_badge": "n",
+      "make_docs": "y",
+      "add_translations": "n",
+      "command_line_interface": "No command-line interface",
+      "create_author_file": "y",
+      "open_source_license": "Apache Software License 2.0",
+      "generated_with_cruft": "y",
+      "__gh_slug": "https://github.com/xarray-contrib/xncml",
+      "_template": "https://github.com/Ouranosinc/cookiecutter-pypackage.git",
+      "_commit": "760bcbb2540bd973d57ea1aa1f1b24759f6d0955"
+    }
+  },
+  "directory": null
+}

.cruft.json

@@ -0,0 +1,24 @@
+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.{yaml,yml}]
+indent_size = 2
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab

.editorconfig

@@ -0,0 +1,27 @@
+[flake8]
+exclude =
+	.eggs,
+	.git,
+	build,
+	docs,
+	tests
+ignore =
+	C,
+	D,
+	E,
+	F,
+	W503
+per-file-ignores =
+rst-roles =
+	doc,
+	mod,
+	py:attr,
+	py:attribute,
+	py:class,
+	py:const,
+	py:data,
+	py:func,
+	py:meth,
+	py:mod,
+	py:obj,
+	py:ref

.flake8

@@ -1,25 +1,11 @@
-Thanks for submitting an issue!
-
-Here's a quick checklist in what to include:
-
-- [ ] Include a detailed description of the bug or suggestion
-- [ ] `conda list` of the conda environment you are using
-- [ ] Minimal, self-contained copy-pastable example that generates the issue if possible. Please be concise with code posted. See guidelines below on how to provide a good bug report:
-
-     -  [Minimal Complete Verifiable Examples](https://stackoverflow.com/help/mcve)
-    -  [Craft Minimal Bug Reports](http://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
-
-    Bug reports that follow these guidelines are easier to diagnose,
-    and so are often handled much more quickly.
-
-
+* xncml version:
+* Python version:
+* Operating System:
 
 ### Description
 
-```
 Describe what you were trying to get done.
 Tell us what happened, what went wrong, and what you expected to happen.
-```
 
 ### What I Did
 

.git_archival.txt

@@ -0,0 +1,34 @@
+name: Generic issue template
+description: For detailing generic/uncategorized issues in xncml
+
+body:
+  - type: textarea
+    id: generic-issue
+    attributes:
+      label: Generic Issue
+      description: Please fill in the following information fields as needed.
+      value: |
+        * xncml version:
+        * Python version:
+        * Operating System:
+
+        ### Description
+        <!--Describe what you were trying to get done.
+        Tell us what happened, what went wrong, and what you expected to happen.-->
+
+        ### What I Did
+        <!--Paste the command(s) you ran and the output.
+        If there was a crash, please include the traceback below.-->
+        ```
+        $ pip install foo --bar
+        ```
+
+        ### What I Received
+        <!--Paste the output or the stack trace of the problem you experienced here.-->
+        ```
+        Traceback (most recent call last):
+         File "/path/to/file/script.py", line 3326, in run_code
+           exec(code_obj, self.user_global_ns, self.user_ns)
+         File "<ipython-input-2-9e1622b385b6>", line 1, in <module>
+           1/0
+         ZeroDivisionError: division by zero

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,44 @@
+name: Bug report
+description: Help us improve xncml
+labels: [ "bug" ]
+
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to fill out this bug report!
+  - type: textarea
+    id: setup-information
+    attributes:
+      label: Setup Information
+      description: |
+        What software versions are you running? Example:
+        - xncml version: 0.55.0-gamma
+        - Python version: 4.2
+        - Operating System: Nutmeg Linux 12.34 | macOS 11.0 "Redmond"
+      value: |
+        - xncml version:
+        - Python version:
+        - Operating System:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description
+      description: Describe what you were trying to get done. Tell us what happened, what went wrong, and what you expected to happen.
+  - type: textarea
+    id: steps-to-reproduce
+    attributes:
+      label: Steps To Reproduce
+      description: Paste the command(s) you ran and the output. If there was a crash, please include the traceback below.
+  - type: textarea
+    id: additional-context
+    attributes:
+      label: Additional context
+      description: Add any other context about the problem here.
+  - type: checkboxes
+    id: submit-pr
+    attributes:
+      label: Contribution
+      description: Do you intend to submit a fix for this bug? (The xncml developers will help with code compliance)
+      options:
+        - label: I would be willing/able to open a Pull Request to address this bug.

.github/ISSUE_TEMPLATE/0001-GENERIC-ISSUE-TEMPLATE.yml

@@ -0,0 +1,31 @@
+name: Feature request
+description: Suggest an idea for xncml
+labels: [ "enhancement" ]
+
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to fill out this feature request!
+  - type: textarea
+    id: problem
+    attributes:
+      label: Addressing a Problem?
+      description: Is your feature request related to a problem? Please describe it.
+  - type: textarea
+    id: potential-solution
+    attributes:
+      label: Potential Solution
+      description: Describe the solution you'd like to see implemented.
+  - type: textarea
+    id: additional-context
+    attributes:
+      label: Additional context
+      description: Add any other context about the feature request here.
+  - type: checkboxes
+    id: submit-pr
+    attributes:
+      label: Contribution
+      description: Do you intend to submit a fix for this bug? (The xncml developers will help with code compliance)
+      options:
+        - label: I would be willing/able to open a Pull Request to contribute this feature.

.github/ISSUE_TEMPLATE/0002-BUG-REPORT.yml

@@ -0,0 +1,23 @@
+name: Question/Support
+description: Ask for help from the developers
+labels: [ "support" ]
+
+body:
+  - type: textarea
+    id: setup-information
+    attributes:
+      label: Setup Information
+      description: |
+        What software versions are you running? Example:
+        - xncml version: 0.55.0-gamma
+        - Python version: 4.2
+        - Operating System: Nutmeg Linux 12.34 | macOS 11.0 "Redmond"
+      value: |
+        - xncml version:
+        - Python version:
+        - Operating System:
+  - type: textarea
+    id: description
+    attributes:
+      label: Context
+      description: Describe what you were trying to get done. Tell us what happened, what went wrong, and what you expected to happen.