Merge branch 'master' into warnings-as-errors

.circleci/ci-oldest-reqs.txt

@@ -2,13 +2,13 @@ click==7.1.2
 coverage==5.3.1
 deprecation==2.0
 filelock==3.0.0
-h5py==2.8.0
-numpy==1.13.3
+h5py==2.9.0
+numpy==1.19.0
 packaging==15.0
 pandas==1.0.0
-pymongo==3.0.0
+pymongo==3.10.0
 pytest-cov==2.10.1
 pytest-xdist==2.5.0
 pytest==6.2.1
-tables==3.4.2
+tables==3.6.1
 tqdm==4.10.0

.circleci/config.yml

@@ -76,7 +76,7 @@ jobs:
           command: |
             . venv/bin/activate
             ${PYTHON} -m pytest -n 2 --dist loadfile --cov=signac --cov-config=setup.cfg --cov-report=xml tests/ -v
-            codecov
+            ${PYTHON} -m codecov
 
       - store_artifacts:
           path: test-reports
@@ -123,10 +123,10 @@ jobs:
       - image: circleci/mongo:latest
       - image: circleci/redis:latest
 
-  linux-python-36-oldest:
+  linux-python-38-oldest:
     <<: *linux-template
     docker:
-      - image: cimg/python:3.6
+      - image: cimg/python:3.8
       - image: circleci/mongo:latest
       - image: circleci/redis:latest
     environment:
@@ -143,18 +143,18 @@ jobs:
       DEPENDENCIES: "NEWEST"
       PYTHON: pypy3
 
-  windows-python-38:
+  windows-python-310:
     executor:
       name: win/default
       shell: bash.exe
     environment:
-      PYTHON: python
+      PYTHON: C:\Python310\python
     steps:
       - checkout
       - run:
           name: Install Python
           command: |
-            choco install python --version 3.8.1 --limit-output --no-progress
+            choco install python --version 3.10.2 --limit-output --no-progress
       - run:
           name: Install dependencies
           command: |
@@ -172,7 +172,7 @@ jobs:
           name: Run tests
           command: |
             ${PYTHON} -m pytest -n 2 --dist loadfile --cov=signac --cov-report=xml tests/ -v
-            codecov
+            ${PYTHON} -m codecov
 
   macos-python-3:
     macos:  # executor type
@@ -196,7 +196,7 @@ jobs:
             python -m pip install --progress-bar off -U -r requirements/requirements-test-optional.txt
             python -m pip install --progress-bar off -U -e .
             python -m pytest -n 2 --dist loadfile --cov=signac --cov-report=xml tests/ -v
-            codecov
+            python -m codecov
 
   check-metadata:
     docker:
@@ -245,9 +245,9 @@ workflows:
       - linux-python-310-minimal
       - linux-python-39
       - linux-python-38
-      - linux-python-36-oldest
+      - linux-python-38-oldest
       - linux-pypy-38
-      - windows-python-38
+      - windows-python-310
       - macos-python-3
       - check-metadata:
           filters:
@@ -262,9 +262,9 @@ workflows:
             - linux-python-310-minimal
             - linux-python-39
             - linux-python-38
-            - linux-python-36-oldest
+            - linux-python-38-oldest
             - linux-pypy-38
-            - windows-python-38
+            - windows-python-310
   deploy:
     jobs:
       - deploy-pypi:

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,4 +1,4 @@
-<!-- Provide a general summary of your changes in the Title above -->
+<!-- Provide a general summary of your changes in the title above. -->
 
 ## Description
 <!-- Describe your changes in detail. -->
@@ -8,7 +8,6 @@
 <!-- Why is this change required? What problem does it solve? -->
 <!-- If it fixes an open issue, please link to the issue here. -->
 
-
 ## Checklist:
 <!-- This checklist must be complete before merging the pull request. -->
 <!-- If you are unsure about any of these items, do not hesitate to ask! -->

.pre-commit-config.yaml

@@ -1,7 +1,11 @@
 ci:
   autoupdate_schedule: quarterly
 
-exclude: '(?:^signac/common/configobj/)'
+exclude: |
+  (?x)^(
+    ^signac/common/configobj/|
+    ^signac/common/deprecation/
+  )
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -23,7 +27,7 @@ repos:
     hooks:
       - id: pyupgrade
         args:
-          - --py36-plus
+          - --py38-plus
   - repo: https://github.com/PyCQA/isort
     rev: '5.10.1'
     hooks:
@@ -45,6 +49,7 @@ repos:
             ^doc/|
             ^tests/|
             ^signac/common/configobj/|
+            ^signac/common/deprecation/|
             ^signac/db/
           )
   - repo: https://github.com/pre-commit/mirrors-mypy

README.md

@@ -30,7 +30,7 @@ This makes it easier to operate on large data spaces, streamlines post-processin
 ## Installation
 
 The recommended installation method for **signac** is through **conda** or **pip**.
-The software is tested for Python 3.6+ and is built for all major platforms.
+The software is tested for Python 3.8+ and is built for all major platforms.
 
 To install **signac** *via* the [conda-forge](https://conda-forge.github.io/) channel, execute:
 

changelog.txt

@@ -22,6 +22,7 @@ Changed
 
  - Schema migration is now performed on directories rather than signac projects and supports a wider range of schemas (#654).
  - Deprecated features now use ``FutureWarning`` instead of ``DeprecationWarning``, which is hidden by default (#687, #691).
+ - Project names have a default in anticipation of removing names entirely. Project names will be removed in signac 2.0 (#644).
 
 Deprecated
 ++++++++++
@@ -33,18 +34,18 @@ Deprecated
  - ``signac.cite`` module is deprecated (#611, #592).
  - ``config.get_config`` method is deprecated (#675).
 
-Changed
-+++++++
-
- - Project names have a default in anticipation of removing names entirely. Project names will be removed in signac 2.0.
-
 Fixed
 +++++
 
  - ``H5Store.mode`` returns the file mode (#607).
  - User-provided path functions now raise an error if not unique (#666).
  - ``Collection`` class no longer raises an error when searching by a primary key that does not exist (#676).
 
+Removed
++++++++
+
+ - Dropped support for Python 3.6 and Python 3.7 (#715) following the recommended support schedules of `NEP 29 <https://numpy.org/neps/nep-0029-deprecation_policy.html>`__.
+
 [1.7.0] -- 2021-06-08
 ---------------------
 

doc/installation.rst

@@ -5,9 +5,9 @@ Installation
 ============
 
 The recommended installation method for **signac** is via conda_ or pip_.
-The software is tested for Python versions 3.6+ and has minimal dependencies.
+The software is tested for Python versions 3.8+ and has minimal dependencies.
 Some features such as the HDF5 integration require additional packages.
-Supported Python and NumPy versions are determined according to the `NEP 29 deprecation policy <https://numpy.org/neps/nep-0029-deprecation_policy.html>`_.
+The signac framework uses the `NEP 29 deprecation policy <https://numpy.org/neps/nep-0029-deprecation_policy.html>`__ as a guideline for when to drop support for Python and NumPy versions, and does not guarantee support beyond the versions recommended in that proposal.
 
 .. _conda: https://conda.io/
 .. _conda-forge: https://conda-forge.org/

pyproject.toml

@@ -1,5 +1,5 @@
 [tool.black]
-target-version = ['py36']
+target-version = ['py38']
 include = '\.pyi?$'
 exclude = '''
 (

setup.py

@@ -47,8 +47,6 @@
         "License :: OSI Approved :: BSD License",
         "Topic :: Database",
         "Topic :: Scientific/Engineering :: Physics",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
@@ -64,7 +62,7 @@
     install_requires=requirements,
     # Supported versions are determined according to NEP 29.
     # https://numpy.org/neps/nep-0029-deprecation_policy.html
-    python_requires=">=3.6, <4",
+    python_requires=">=3.8, <4",
     extras_require={"db": ["pymongo>=3.0"], "mpi": ["mpi4py"], "h5": ["h5py"]},
     entry_points={"console_scripts": ["signac = signac.__main__:main"]},
 )