Release/1.5.1 (#441)

* Update changelog.

* Update pre-commit hooks.

* Move requirements-dev.txt to requirements-test.txt to reflect that its purpose is only for CI.

* Use pip>=20.3.

* Bump up to version 1.5.1.

.circleci/config.yml

@@ -10,10 +10,10 @@ orbs:
 references:
   restore_keys: &restore_keys
     keys:
-      - python-env-v7-{{ arch }}-{{ .Environment.CIRCLE_JOB }}-{{ checksum "setup.py" }}-{{ checksum "requirements-dev.txt" }}-{{ checksum "requirements-precommit.txt" }}-{{ checksum ".pre-commit-config.yaml" }}
+      - python-env-v7-{{ arch }}-{{ .Environment.CIRCLE_JOB }}-{{ checksum "setup.py" }}-{{ checksum "requirements-test.txt" }}-{{ checksum "requirements-precommit.txt" }}-{{ checksum ".pre-commit-config.yaml" }}
 
   save_key: &save_key
-    key: python-env-v7-{{ arch }}-{{ .Environment.CIRCLE_JOB }}-{{ checksum "setup.py" }}-{{ checksum "requirements-dev.txt" }}-{{ checksum "requirements-precommit.txt" }}-{{ checksum ".pre-commit-config.yaml" }}
+    key: python-env-v7-{{ arch }}-{{ .Environment.CIRCLE_JOB }}-{{ checksum "setup.py" }}-{{ checksum "requirements-test.txt" }}-{{ checksum "requirements-precommit.txt" }}-{{ checksum ".pre-commit-config.yaml" }}
 
 jobs:
   pre-checks:
@@ -70,9 +70,9 @@ jobs:
             if [[ "${CIRCLE_JOB}" != *"pypy"* ]]; then
               sudo apt update -qq && sudo apt install -y -qq libhdf5-dev
             fi
-            ${PYTHON} -m pip install --progress-bar off -U pip==20.2
+            ${PYTHON} -m pip install --progress-bar off -U pip>=20.3
             ${PYTHON} -m pip install --progress-bar off -U codecov
-            ${PYTHON} -m pip install --progress-bar off -U -e . -r requirements-dev.txt
+            ${PYTHON} -m pip install --progress-bar off -U -e . -r requirements-test.txt
 
       - save_cache:
           <<: *save_key
@@ -144,7 +144,7 @@ jobs:
           name: Install dependencies
           command: |
             ${PYTHON} -m pip install --progress-bar off -U codecov
-            ${PYTHON} -m pip install --progress-bar off -U -e . -r requirements-dev.txt
+            ${PYTHON} -m pip install --progress-bar off -U -e . -r requirements-test.txt
       - run:
           name: Run tests
           command: |
@@ -168,7 +168,7 @@ jobs:
             . test_env/bin/activate
             python --version
             python -m pip install --progress-bar off -U codecov
-            python -m pip install --progress-bar off -U -e . -r requirements-dev.txt
+            python -m pip install --progress-bar off -U -e . -r requirements-test.txt
             python -m pytest --cov=signac --cov-report=xml tests/ -v
             codecov
 

.circleci/deploy.bash

@@ -3,7 +3,7 @@
 set -e
 set -u
 
-python -m pip install --progress-bar off --user -U -r requirements-dev.txt
+python -m pip install --progress-bar off --user -U -r requirements-test.txt
 python -m pip install --progress-bar off --user -U twine wheel setuptools
 
 # PYPI_USERNAME - (Required) Username for the publisher's account on PyPI

.pre-commit-config.yaml

@@ -1,14 +1,19 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 'v3.3.0'
+    rev: 'v3.4.0'
     hooks:
       - id: end-of-file-fixer
         exclude: 'setup.cfg'
       - id: trailing-whitespace
         exclude: 'setup.cfg'
+      - id: check-builtin-literals
+      - id: check-executables-have-shebangs
+      - id: check-json
+      - id: check-yaml
       - id: debug-statements
+      - id: requirements-txt-fixer
   - repo: https://github.com/asottile/pyupgrade
-    rev: 'v2.7.3'
+    rev: 'v2.7.4'
     hooks:
       - id: pyupgrade
         exclude: '(?:configobj/.*)'

.zenodo.json

@@ -124,5 +124,5 @@
         "id": "http://www.opensource.org/licenses/BSD-3-Clause"
     },
     "title": "signac",
-    "version": "1.5.0"
+    "version": "1.5.1"
 }

CITATION.cff

@@ -2,7 +2,7 @@
 ---
 cff-version: "1.0.3"
 title: signac
-version: 1.5.0
+version: 1.5.1
 abstract: |
     The signac framework helps users manage and scale file-based workflows, facilitating data
     reuse, sharing, and reproducibility. It provides a simple and robust data model to create

benchmark.py

@@ -75,7 +75,7 @@ def calc_project_metadata_size(project):
 
 def get_partition(path):
     path = os.path.realpath(path)
-    candidates = dict()
+    candidates = {}
     for partition in psutil.disk_partitions(all=True):
         mp = os.path.realpath(partition.mountpoint)
         if path.startswith(mp):

changelog.txt

@@ -7,8 +7,8 @@ The **signac** package follows `semantic versioning <https://semver.org/>`_.
 Version 1
 =========
 
-next
-----
+[1.5.1] -- 2020-12-19
+---------------------
 
 Added
 +++++

doc/conf.py

@@ -80,9 +80,9 @@ def __getattr__(cls, name):
 # built documents.
 #
 # The short X.Y version.
-version = "1.5.0"
+version = "1.5.1"
 # The full version, including alpha/beta/rc tags.
-release = "1.5.0"
+release = "1.5.1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/requirements.txt

@@ -1,6 +1,6 @@
-nbconvert
-nbsphinx>=0.3
+deprecation>=2
 IPython
 jupyter_client
-deprecation>=2
+nbconvert
+nbsphinx>=0.3
 sphinxcontrib-programoutput

doc/support.rst

@@ -46,7 +46,7 @@ Then clone your fork and install the package from source with:
 .. code-block:: bash
 
     (signac-dev) ~ $ cd path/to/my/fork/of/signac
-    (signac-dev) signac $ pip install -e . -r requirements-dev.txt
+    (signac-dev) signac $ pip install -e .
 
 The ``-e`` option stands for *editable*, which means that the package is directly loaded from the source code repository.
 That means any changes made to the source code are immediately reflected upon reloading the Python interpreter.

requirements-benchmark.txt

@@ -1,6 +1,6 @@
 click>=7.0
-numpy==1.19.4
 gitdb2==4.0.2
 GitPython==3.1.11
+numpy==1.19.4
 pandas==1.1.4; implementation_name=='cpython' --no-binary :none:
 psutil==5.7.3

requirements-dev.txt → requirements-test.txt

@@ -4,7 +4,7 @@ h5py==3.1.0; implementation_name=='cpython'
 numpy==1.19.4
 pandas==1.1.4; implementation_name=='cpython'
 pymongo==3.11.1; implementation_name=='cpython'
-pytest-cov==2.10.1
 pytest==6.1.2
+pytest-cov==2.10.1
 ruamel.yaml==0.16.12
 tables==3.6.1; implementation_name=='cpython'

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.5.0
+current_version = 1.5.1
 commit = True
 tag = False
 message = Bump up to version {new_version}.
@@ -13,9 +13,7 @@ python-tag = py3
 [flake8]
 max-line-length = 100
 exclude = configobj
-# Use select to ignore unwanted flake8 plugins
 select = E,F,W
-# Specify errors to ignore by default
 ignore = E123,E126,E203,E226,E241,E704,W503,W504
 
 [pydocstyle]

setup.py

@@ -28,7 +28,7 @@
 
 setup(
     name="signac",
-    version="1.5.0",
+    version="1.5.1",
     packages=find_packages(),
     zip_safe=True,
     maintainer="signac Developers",

signac/__main__.py

@@ -635,7 +635,7 @@ def _main_import_interactive(project, origin, args):
         with _prepare_import_into_project(
             origin, tmp_project, args.schema_path
         ) as data_mapping:
-            paths = dict()
+            paths = {}
             for src, copy_executor in tqdm(
                 dict(data_mapping).items(), desc="Import to temporary project"
             ):
@@ -671,7 +671,7 @@ def _main_import_non_interactive(project, origin, args):
     from .contrib.import_export import _prepare_import_into_project
 
     try:
-        paths = dict()
+        paths = {}
         if args.sync:
             with project.temporary_project() as tmp_project:
                 _print_err("Prepare data space for import...")
@@ -738,7 +738,7 @@ def main_export(args):
     project = get_project()
     jobs = [project.open_job(id=job_id) for job_id in find_with_filter(args)]
 
-    paths = dict()
+    paths = {}
     with tqdm(total=len(jobs), desc="Export") as pbar:
         try:
             for src, dst in export_jobs(
@@ -919,7 +919,7 @@ def main_config_set(args):
             args.value = args.value[0]
     sec = cfg
     for key in keys[:-1]:
-        sec = sec.setdefault(key, dict())
+        sec = sec.setdefault(key, {})
     try:
         sec[keys[-1]] = args.value
         _print_err(f"Updated value '{args.key}'='{args.value}'.")
@@ -959,7 +959,7 @@ def main_config_host(args):
         cfg = config.get_config(fn_config)
 
     def hostcfg():
-        return cfg.setdefault("hosts", dict()).setdefault(args.hostname, dict())
+        return cfg.setdefault("hosts", {}).setdefault(args.hostname, {})
 
     if sum((args.test, args.remove, args.show_pw)) > 1:
         raise ValueError(

signac/common/crypt.py

@@ -66,7 +66,7 @@ class SimpleKeyring:
     """Simple in-memory keyring for caching."""
 
     def __init__(self):
-        self._cache = dict()
+        self._cache = {}
 
     @classmethod
     def _encode(cls, msg):

signac/common/host.py

@@ -18,7 +18,7 @@
 
 
 SESSION_PASSWORD_HASH_CACHE = SimpleKeyring()
-SESSION_USERNAME_CACHE = dict()  # type: ignore
+SESSION_USERNAME_CACHE = {}  # type: ignore
 
 """
 THIS MODULE IS DEPRECATED!

signac/contrib/collection.py

@@ -450,9 +450,9 @@ def __init__(self, docs=None, primary_key="_id", compresslevel=0, _trust=False):
         self._compresslevel = compresslevel
         self._requires_flush = False
         self._dirty = set()
-        self._indexes = dict()
+        self._indexes = {}
         self._next_default_id_ = None
-        self._docs = dict()
+        self._docs = {}
         if docs is not None:
             for doc in docs:
                 if self._primary_key not in doc:

signac/contrib/filesystems.py

@@ -24,7 +24,7 @@
     GRIDFS = True
 
 GRIDFS_LARGE_FILE_WARNING_THRSHLD = int(1e9)  # 1GB
-FILESYSTEM_REGISTRY = dict()
+FILESYSTEM_REGISTRY = {}
 
 """
 THIS MODULE IS DEPRECATED!

signac/contrib/filterparse.py

@@ -220,7 +220,7 @@ def parse_filter_arg(args, file=sys.stderr):
         else:
             return _with_message(_parse_simple(args[0]), file)
     else:
-        q = dict()
+        q = {}
         for i in range(0, len(args), 2):
             key = args[i]
             if i + 1 < len(args):

signac/contrib/import_export.py

@@ -66,7 +66,7 @@ def _make_schema_based_path_function(jobs, exclude_keys=None, delimiter_nested="
     jsi = _build_job_statepoint_index(exclude_const=True, index=index)
     sp_index = OrderedDict(jsi)
 
-    paths = dict()
+    paths = {}
     for key_tokens, values in sp_index.items():
         key = key_tokens.replace(".", delimiter_nested)
         if exclude_keys and key in exclude_keys:
@@ -548,7 +548,7 @@ def _convert_schema_path_to_regex(schema_path):
     # in the schema path.
     re_key_type_field = r"\{(?P<key>[\.\w]+)(?::(?P<type>[a-z]+))?\}"
     schema_regex = ""  # the return value
-    types = dict()  # maps values to their designated types
+    types = {}  # maps values to their designated types
     index = 0
     while True:
         m = re.search(re_key_type_field, schema_path[index:])
@@ -948,7 +948,7 @@ def read_sp_manifest_file(path):
     else:
         raise TypeError("The schema variable must be None, callable, or a string.")
 
-    mappings = dict()
+    mappings = {}
     skip_subdirs = set()
 
     dirs = {os.path.dirname(name) for name in names}
@@ -1097,7 +1097,7 @@ def read_sp_manifest_file(path):
     else:
         raise TypeError("The schema variable must be None, callable, or a string.")
 
-    mappings = dict()
+    mappings = {}
     skip_subdirs = set()
 
     dirs = [member.name for member in tarfile.getmembers() if member.isdir()]

signac/contrib/indexing.py

@@ -168,7 +168,7 @@ class RegexFileCrawler(BaseCrawler):
         MyCrawler.define('.*\/a_(?P<a>\d+)\.txt', 'TextFile')
     """
     "Mapping of compiled regex objects and associated formats."
-    definitions = dict()  # type: ignore
+    definitions = {}  # type: ignore
 
     @classmethod
     @deprecated(
@@ -302,8 +302,9 @@ def process(self, doc, dirpath, fn):
         :param fn: The filename.
         :type fn: str
         :returns: An index document, that means an instance of mapping.
-        :rtype: mapping"""
-        result = dict()
+        :rtype: mapping
+        """
+        result = {}
         for key, value in doc.items():
             if value is None or isinstance(value, bool):
                 result[key] = value
@@ -430,7 +431,7 @@ def __init__(self, root):
         from .project import get_project
 
         root = get_project(root=root).workspace()
-        self._statepoints = dict()
+        self._statepoints = {}
         return super().__init__(root=root)
 
     def _get_job_id(self, dirpath):

signac/contrib/job.py

@@ -102,7 +102,7 @@ def __init__(self, project, statepoint, _id=None):
         self._stores = H5StoreManager(self._wd)
 
         # Prepare current working directory for context management
-        self._cwd = list()
+        self._cwd = []
 
     @deprecated(
         deprecated_in="1.3",
@@ -210,7 +210,7 @@ def reset_statepoint(self, new_statepoint):
         self._fn_doc = dst._fn_doc
         self._document = None
         self._data = None
-        self._cwd = list()
+        self._cwd = []
         logger.info(f"Moved '{self}' -> '{dst}'.")
 
     def _reset_sp(self, new_sp=None):

signac/contrib/linked_view.py

@@ -100,7 +100,7 @@ def create_linked_view(project, prefix=None, job_ids=None, index=None, path=None
 
     path_function = _make_path_function(jobs, path)
 
-    links = dict()
+    links = {}
     for job in jobs:
         paths = os.path.join(path_function(job), "job")
         links[paths] = job.workspace()
@@ -251,7 +251,7 @@ class _Node:
     def __init__(self, name=None, value=None):
         self.name = name
         self.value = value
-        self.children = dict()
+        self.children = {}
 
     def get_child(self, name):
         """Get child node corresponding to the name passed.
@@ -316,7 +316,7 @@ def _get_branches(root, branch=None):
 
     """
     if branch is None:
-        branch = list()
+        branch = []
     else:
         branch = list(branch) + [root]
     if root.children:
@@ -362,7 +362,7 @@ def _find_dead_branches(root, branch=None):
 
     """
     if branch is None:
-        branch = list()
+        branch = []
     else:
         branch = list(branch) + [root]
     if root.children: