Warning about repo being archived (#344)

* add DeprecationWarning on import * big wrarning in README * add big fat warning to docs landing page too * try adding prolog to every page * rearrange emojis * try updating micromamba action * also update micromamba for other job * fix expected repr diff * pin xarray * pin to earlier version * upgrade the python version for docs * require a more recent version of `sphinx` * replace `sphinx-panels` with `sphinx-design` * disable the mypy hook * autoupdate hook versions * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * ignore `flake8` errors that conflict with `black` * update link in warning to release discussion upstream * update links --------- Co-authored-by: Justus Magin <keewis@posteo.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
xarray-contrib · Oct 24, 2024 · 5f3956f · 5f3956f
1 parent d97b636
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diff --git a/.flake8 b/.flake8
@@ -10,6 +10,8 @@ ignore =
     E731
     # line break before binary operator
     W503
+    E701
+    E704
 exclude=
     .eggs
     doc
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -25,12 +25,12 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Create conda environment
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
           cache-downloads: true
           micromamba-version: 'latest'
           environment-file: ci/environment.yml
-          extra-specs: |
+          create-args: >-
             python=${{ matrix.python-version }}
 
       - name: Conda info
@@ -70,12 +70,12 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Create conda environment
-        uses: mamba-org/provision-with-micromamba@main
+        uses: mamba-org/setup-micromamba@v1
         with:
           cache-downloads: true
           micromamba-version: 'latest'
           environment-file: ci/environment.yml
-          extra-specs: |
+          create-args: >-
             python=${{ matrix.python-version }}
 
       - name: Conda info

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -15,38 +15,38 @@ repos:
       - id: isort
   # https://github.com/python/black#version-control-integration
   - repo: https://github.com/psf/black
-    rev: 23.12.1
+    rev: 24.10.0
     hooks:
       - id: black
   - repo: https://github.com/keewis/blackdoc
     rev: v0.3.9
     hooks:
       - id: blackdoc
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.1.1
     hooks:
       - id: flake8
   # - repo: https://github.com/Carreau/velin
   #   rev: 0.0.8
   #   hooks:
   #     - id: velin
   #       args: ["--write", "--compact"]
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.8.0
-    hooks:
-      - id: mypy
-        # Copied from setup.cfg
-        exclude: "properties|asv_bench|docs"
-        additional_dependencies: [
-            # Type stubs
-            types-python-dateutil,
-            types-pkg_resources,
-            types-PyYAML,
-            types-pytz,
-            # Dependencies that are typed
-            numpy,
-            typing-extensions>=4.1.0,
-          ]
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: v1.13.0
+  #   hooks:
+  #     - id: mypy
+  #       # Copied from setup.cfg
+  #       exclude: "properties|asv_bench|docs"
+  #       additional_dependencies: [
+  #           # Type stubs
+  #           types-python-dateutil,
+  #           types-pkg_resources,
+  #           types-PyYAML,
+  #           types-pytz,
+  #           # Dependencies that are typed
+  #           numpy,
+  #           typing-extensions>=4.1.0,
+  #         ]
   # run this occasionally, ref discussion https://github.com/pydata/xarray/pull/3194
   # - repo: https://github.com/asottile/pyupgrade
   #   rev: v1.22.1

diff --git a/README.md b/README.md
@@ -14,13 +14,17 @@ that was more flexible than a single `xarray.Dataset` object.
 The initial motivation was to represent netCDF files / Zarr stores with multiple nested groups in a single in-memory object,
 but `datatree.DataTree` objects have many other uses.
 
-### DEPRECATION NOTICE
+# :rotating_light: :bell: :warning: NO LONGER MAINTAINED :warning: :bell: :rotating_light:
 
-Datatree is in the process of being merged upstream into xarray (as of [v0.0.14](https://github.com/xarray-contrib/datatree/releases/tag/v0.0.14), see xarray issue [#8572](https://github.com/pydata/xarray/issues/8572)). We are aiming to preserve the record of contributions to this repository during the migration process. However whilst we will hapily accept new PRs to this repository, this repo will be deprecated and any PRs since [v0.0.14](https://github.com/xarray-contrib/datatree/releases/tag/v0.0.14) might be later copied across to xarray without full git attribution.
+**This repository has been archived and the code is no longer maintained!**
 
-Hopefully for users the disruption will be minimal - and just mean that in some future version of xarray you only need to do `from xarray import DataTree` rather than `from datatree import DataTree`. Once the migration is complete this repository will be archived.
+Datatree has been [merged upstream into `pydata/xarray`](https://github.com/pydata/xarray/issues/8572), and released as of xarray version `2024.10.0`.
 
-PLEASE RAISE NEW ISSUES ON THE XARRAY REPOSITORY UPSTREAM
+There will be no further bugfixes or feature additions to this respository.
+
+Users of this repository should migrate to using `xarray.DataTree` instead, following the [Migration Guide](https://github.com/pydata/xarray/discussions/9680).
+
+The information below is all outdated, and is left only for historical interest.
 
 ### Installation
 You can install datatree via pip:

diff --git a/ci/doc.yml b/ci/doc.yml
@@ -3,12 +3,12 @@ channels:
   - conda-forge
 dependencies:
   - pip
-  - python>=3.9
+  - python>=3.12
   - netcdf4
   - scipy
-  - sphinx>=4.2.0
+  - sphinx>=6.0.0
   - sphinx-copybutton
-  - sphinx-panels
+  - sphinx-design
   - sphinx-autosummary-accessors
   - sphinx-book-theme >= 0.0.38
   - nbsphinx
@@ -18,7 +18,7 @@ dependencies:
   - ipython
   - h5netcdf
   - zarr
-  - xarray
+  - "xarray>=2022.06.0, <=2024.07.0"
   - pip:
       - -e ..
       - sphinxext-rediraffe

diff --git a/ci/environment.yml b/ci/environment.yml
@@ -13,4 +13,4 @@ dependencies:
   - h5netcdf
   - zarr
   - pip:
-      - xarray>=2022.05.0.dev0
+      - "xarray>=2022.06.0, <=2024.07.0"
diff --git a/datatree/__init__.py b/datatree/__init__.py
@@ -1,10 +1,20 @@
+import warnings
+
 # import public API
 from .datatree import DataTree
 from .extensions import register_datatree_accessor
 from .io import open_datatree
 from .mapping import TreeIsomorphismError, map_over_subtree
 from .treenode import InvalidTreeError, NotFoundInTreeError
 
+warnings.warn(
+    "The repository `xarray-contrib/datatree` has been archived! It is no longer maintained as of October 2024. "
+    "Datatree functionality has been migrated upstream to `pydata/xarray`, so please use `xarray.DataTree` instead. "
+    "To help you migrate a guide can be found by following https://github.com/pydata/xarray/discussions/9680",
+    DeprecationWarning,
+)
+
+
 try:
     # NOTE: the `_version.py` file must not be present in the git repository
     #   as it is generated by setuptools at install time

diff --git a/datatree/datatree.py b/datatree/datatree.py
@@ -177,8 +177,7 @@ def __getitem__(self, key: Hashable) -> DataArray:  # type: ignore[misc]
         ...
 
     @overload
-    def __getitem__(self, key: Any) -> Dataset:
-        ...
+    def __getitem__(self, key: Any) -> Dataset: ...
 
     def __getitem__(self, key) -> DataArray:
         # TODO call the `_get_item` method of DataTree to allow path-like access to contents of other nodes

diff --git a/datatree/formatting_html.py b/datatree/formatting_html.py
@@ -22,9 +22,11 @@ def summarize_children(children: Mapping[str, Any]) -> str:
     lines_callback = lambda n, c, end: _wrap_repr(node_repr(n, c), end=end)
 
     children_html = "".join(
-        lines_callback(n, c, end=False)  # Long lines
-        if i < N_CHILDREN
-        else lines_callback(n, c, end=True)  # Short lines
+        (
+            lines_callback(n, c, end=False)  # Long lines
+            if i < N_CHILDREN
+            else lines_callback(n, c, end=True)
+        )  # Short lines
         for i, (n, c) in enumerate(children.items())
     )
 

diff --git a/datatree/iterators.py b/datatree/iterators.py
@@ -60,8 +60,7 @@ def __next__(self) -> Iterator[Tree]:
 
     @staticmethod
     @abstractmethod
-    def _iter(children: List[Tree], filter_, stop, maxlevel) -> Iterator[Tree]:
-        ...
+    def _iter(children: List[Tree], filter_, stop, maxlevel) -> Iterator[Tree]: ...
 
     @staticmethod
     def _abort_at_level(level, maxlevel):

diff --git a/datatree/tests/test_datatree.py b/datatree/tests/test_datatree.py
@@ -166,8 +166,7 @@ def test_assign_when_already_child_with_variables_name(self):
             dt.ds = new_ds
 
 
-class TestGet:
-    ...
+class TestGet: ...
 
 
 class TestGetItem:
@@ -450,8 +449,7 @@ def test_setitem_dataarray_replace_existing_node(self):
         xrt.assert_identical(results.to_dataset(), expected)
 
 
-class TestDictionaryInterface:
-    ...
+class TestDictionaryInterface: ...
 
 
 class TestTreeFromDict:

diff --git a/datatree/tests/test_formatting.py b/datatree/tests/test_formatting.py
@@ -108,13 +108,13 @@ def test_diff_node_data(self):
         Data in nodes at position '/a' do not match:
 
         Data variables only on the left object:
-            v        int64 1
+            v        int64 8B 1
 
         Data in nodes at position '/a/b' do not match:
 
         Differing data variables:
-        L   w        int64 5
-        R   w        int64 6"""
+        L   w        int64 8B 5
+        R   w        int64 8B 6"""
         )
         actual = diff_tree_repr(dt_1, dt_2, "equals")
         assert actual == expected
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -30,6 +30,11 @@
 parent = os.path.dirname(cwd)
 sys.path.insert(0, parent)
 
+# -- Deprecation Warning banner -----------------------------------------------------
+
+rst_prolog = """.. attention::
+    This repository has been archived. Please use xarray.DataTree instead.
+"""
 
 # -- General configuration -----------------------------------------------------
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -5,6 +5,18 @@ Datatree
 
 **Datatree is a prototype implementation of a tree-like hierarchical data structure for xarray.**
 
+# !!! NO LONGER MAINTAINED !!!
+
+**This repository has been archived and the code is no longer maintained!**
+
+Datatree has been `merged upstream into pydata/xarray <https://github.com/pydata/xarray/issues/8572>`_, and released as of xarray version `2024.10.0`.
+
+There will be no further bugfixes or feature additions to this respository.
+
+Users of this repository should migrate to using `xarray.DataTree` instead, following the `Migration Guide <https://github.com/pydata/xarray/discussions/9680>`_.
+
+The information below is all outdated, and is left only for historical interest.
+
 Why Datatree?
 ~~~~~~~~~~~~~
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -19,7 +19,7 @@ classifiers = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    "xarray >=2023.12.0",
+    "xarray >=2023.12.0, <=2024.07.0",
     "packaging",
 ]
 dynamic = ["version"]