Use synced_collections. (#924)

* Use synced_collections.

* Add changelog entry.

* Use PyPI release.

* Update doc intersphinx links, pre-commit hooks, GitHub Actions, and test requirements to remove unneeded dependencies.

* Fix warning from changelog syntax.

* Update changelog.txt

Co-authored-by: Tommy Waltmann <53307607+tommy-waltmann@users.noreply.github.com>

---------

Co-authored-by: Tommy Waltmann <53307607+tommy-waltmann@users.noreply.github.com>

.github/workflows/ci-oldest-reqs.txt

@@ -5,7 +5,6 @@ h5py==2.10.0
 numpy==1.19.0
 packaging==15.0
 pandas==1.0.0
-pymongo==3.10.0
 pytest==6.2.1
 pytest-cov==2.10.1
 pytest-xdist==2.5.0

.github/workflows/publish-packages.yml

@@ -40,10 +40,6 @@ jobs:
     - name: Install wheel
       run:
         python -m pip install signac --progress-bar off --no-index -f dist/
-    - name: Run MongoDB
-      uses: supercharge/mongodb-github-action@1.9.0
-    - name: Run Redis
-      uses: supercharge/redis-github-action@1.5.0
     - name: Test with pytest
       run:
         python -m pytest -v tests/

.github/workflows/run-pytest.yml

@@ -53,12 +53,6 @@ jobs:
     - name: Install the package
       run: |
         pip install -e .
-    - name: Run MongoDB
-      uses: supercharge/mongodb-github-action@1.9.0
-      if: ${{ matrix.os == 'ubuntu-latest' && matrix.config.dependencies != 'minimal' }}
-    - name: Run Redis
-      uses: supercharge/redis-github-action@1.5.0
-      if: ${{ matrix.os == 'ubuntu-latest' && matrix.config.dependencies != 'minimal' }}
     - name: Test with pytest
       run: |
         pytest --cov=signac --cov-config=pyproject.toml --cov-report=xml tests/ -v

.pre-commit-config.yaml

@@ -51,4 +51,3 @@ repos:
       - id: mypy
         additional_dependencies:
           - types-filelock
-          - types-redis

changelog.txt

@@ -7,6 +7,14 @@ The **signac** package follows `semantic versioning <https://semver.org/>`_.
 Version 2
 =========
 
+[2.1.0] -- 2023-XX-XX
+---------------------
+
+Changed
++++++++
+
+ - signac's "synced collections" backend used for reading/writing JSON files has been moved to a separate package called ``synced_collections``. See https://github.com/glotzerlab/synced_collections (#924).
+
 [2.0.0] -- 2023-03-30
 ---------------------
 
@@ -94,7 +102,7 @@ Changed
  - Project names have a default in anticipation of removing names entirely. Project names will be removed in signac 2.0 (#644).
  - ``Project.workspace`` is now a property, not a method (#685).
  - Continuous integration uses GitHub Actions instead of CircleCI (#776, #788).
- - Raise errors in testing when ``DeprecatedWarning``s or ``FutureWarning``s are raised (#713).
+ - Raise errors in testing when ``DeprecatedWarning`` or ``FutureWarning`` is raised (#713).
  - Change GitHub PR to check for uncompleted tasks (i.e. unchecked checkboxes) (#686).
 
 Deprecated

doc/api.rst

@@ -158,14 +158,6 @@ signac.sync module
     :undoc-members:
     :show-inheritance:
 
-signac.warnings module
-----------------------
-
-.. automodule:: signac.warnings
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 signac.errors module
 --------------------
 

doc/conf.py

@@ -9,27 +9,8 @@
 to show the default.
 """
 
-import sys
-from unittest.mock import MagicMock
-
 import sphinx_rtd_theme
 
-
-class Mock(MagicMock):
-    """Mocks modules and their contained objects."""
-
-    @classmethod
-    def __getattr__(cls, name):
-        if name == "_mock_methods":
-            return []
-        if name == "version_tuple":
-            return (3, 0)
-        return Mock()
-
-
-MOCK_MODULES = ["pymongo"]
-sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
-
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -87,7 +68,7 @@ def __getattr__(cls, name):
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
@@ -316,10 +297,11 @@ def __getattr__(cls, name):
 
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),
-    "pymongo": ("https://pymongo.readthedocs.io/en/stable/", None),
+    "synced_collections": (
+        "https://docs.signac.io/projects/synced-collections/en/latest/",
+        None,
+    ),
     "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
     "h5py": ("https://docs.h5py.org/en/stable/", None),
-    "zarr": ("https://zarr.readthedocs.io/en/stable", None),
-    "redis": ("https://redis-py.readthedocs.io/en/stable/", None),
     "numcodecs": ("https://numcodecs.readthedocs.io/en/stable/", None),
 }

pyproject.toml

@@ -35,6 +35,8 @@ dependencies = [
     "filelock>=3.0",
     # Used for version parsing and comparison
     "packaging>=15.0",
+    # Synced collections for signac's backend
+    "synced_collections>=1.0.0",
     # Progress bars
     "tqdm>=4.10.0",
 ]

requirements.txt

@@ -1,3 +1,4 @@
 filelock>=3.0
 packaging>=15.0
+synced_collections>=1.0.0
 tqdm>=4.10.0

requirements/requirements-test-optional.txt

@@ -1,8 +1,5 @@
 h5py==3.8.0; implementation_name=='cpython'
 numpy==1.24.3
 pandas==2.0.1; implementation_name=='cpython'
-pymongo==4.3.3; implementation_name=='cpython'
-redis==4.5.4
 ruamel.yaml==0.17.21
 tables==3.8.0; implementation_name=='cpython'
-zarr==2.14.2; platform_system!='Windows'

signac/__init__.py

@@ -9,10 +9,9 @@
 collectively accessible.
 """
 
+from synced_collections.backends.collection_json import BufferedJSONAttrDict as JSONDict
+
 from . import errors, sync
-from ._synced_collections.backends.collection_json import (
-    BufferedJSONAttrDict as JSONDict,
-)
 from .diff import diff_jobs
 from .h5store import H5Store, H5StoreManager
 from .project import Project, TemporaryProject, get_job, get_project, init_project