added notes and deprecations throughout project (#220)

* added notes and deprecations in the project module

* fixed code style formatting problems in project.py

* quick fix for the __version__ variable

* fixed code formatting

* added deprecation package to test environment

* marked everything in contrib/filesystems.py for deprecation

* formatted filesystems.py

* added deprecated tags for mpipool module

* marked unused functions for deprecations in contrib/utility.py

* deprecations in core/utility

* removed one of the copied versions of TemporaryDirectory

* fixed some indentations

* fixed error with python 2.7 compatibility

* added deprecations in connection.py

* updated code format in connection.py

* added deprecations in crypt.py

* added deprecations in host.py

* changed deprecation warnings in crypt.py

* changed deprecation warnings in connection.py

* changed deprecation warnings in host.py

* updated deprecation warnings in filesystems.py

* deprecated the indexing module

* fixed typo

* deprecated the mpipool module

* deprecated everything in the db package

* reworded some depreation notices

* undeprecated some stuff i accidentally deprecated

* undeprecated some stuff I accidentally deprecated

* deprecated the database module

* defined __version__ in smaller number of places

* finshed deprecation annotation stuff

* fixed order for multiple decorators

* removed reference to sublime project files in the git ignore

* moved the __version__ variable to be stored in a single file

* fixed code formatting issues

* updated @deprecated headers in indexing

* standardized the way we deprecate class and functions wrt privacy

* Revert changes to benchmark.py

* Change bumpversion configuration to point to new version.py file.

* Add deprecation to package requirements.

* removed previous whitespace changed

* removed other whitespace change

* updated deprecation style

* fixed flake8 issues

* added myself to list of contributors

* fixed typo in contributors

* removed TODO from check() method in Project class

* added that period in project module

* moved implementation of find_job_ids to private method

* updated the unit test that was failing on py27

* changed the message on a deprecation warning

* refactored internal uses of find_job_ids

* Update signac/contrib/project.py

* Update signac/contrib/project.py

* Update signac/core/utility.py

Co-Authored-By: Carl Simon Adorf <csadorf@umich.edu>

* Update signac/version.py

Co-Authored-By: Carl Simon Adorf <csadorf@umich.edu>

* Un-deprecate JobSearchIndex.find_job_ids.

.bumpversion.cfg

@@ -6,7 +6,7 @@ message = Bump up to version {new_version}.
 
 [bumpversion:file:setup.py]
 
-[bumpversion:file:signac/__init__.py]
+[bumpversion:file:signac/version.py]
 
 [bumpversion:file:doc/conf.py]
 

contributors.yaml

@@ -52,4 +52,9 @@ contributors:
     family-names: Adams
     given-names: Alexander
     affiliation: "University of Michigan"
+  -
+    family-names: Waltmann
+    given-names: "Thomas R."
+    affiliation: "University of Michigan"
+    orcid: "https://orcid.org/0000-0001-6876-5956"
 ...

requirements.txt

@@ -0,0 +1 @@
+deprecation>=2

setup.py

@@ -1,6 +1,12 @@
 import os
 from setuptools import setup, find_packages
 
+
+requirements = [
+    # Deprecation management
+    'deprecation>=2',
+]
+
 description = "Simple file data management database."
 
 try:
@@ -39,6 +45,8 @@
         "Programming Language :: Python :: Implementation :: PyPy",
     ],
 
+    install_requires=requirements,
+
     python_requires='>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, <4',
 
     extras_require={

signac/__init__.py

@@ -44,10 +44,9 @@
 from .core.jsondict import JSONDict
 from .core.h5store import H5Store
 from .core.h5store import H5StoreManager
+from .version import __version__
 
 
-__version__ = '1.2.0'
-
 __all__ = ['__version__', 'contrib', 'db', 'errors', 'warnings', 'sync',
            'cite',
            'Project', 'TemporaryProject', 'get_project', 'init_project', 'get_job',

signac/__main__.py

@@ -27,7 +27,7 @@
     READLINE = True
 
 from . import Project, get_project, init_project, index
-from . import __version__
+from .version import __version__
 from .common import config
 from .common.configobj import flatten_errors, Section
 from .common.crypt import get_crypt_context, parse_pwhash, get_keyring

signac/common/connection.py

@@ -4,10 +4,12 @@
 import subprocess
 import logging
 from os.path import expanduser
+from deprecation import deprecated
 
 import pymongo
 
 from .errors import ConfigError
+from ..version import __version__
 
 
 PYMONGO_2 = pymongo.version_tuple[0] == 2
@@ -19,7 +21,13 @@
 AUTH_SSL = 'SSL'
 AUTH_SSL_x509 = 'SSL-x509'
 
+"""
+THIS MODULE IS DEPRECATED!
+"""
 
+
+@deprecated(deprecated_in="1.3", removed_in="2.0", current_version=__version__,
+            details="The connection module is deprecated.")
 def get_subject_from_certificate(fn_certificate):  # pragma no cover
     try:
         cert_txt = subprocess.check_output(
@@ -34,11 +42,15 @@ def get_subject_from_certificate(fn_certificate):  # pragma no cover
         return lines[0][len('subject='):].strip()
 
 
+@deprecated(deprecated_in="1.3", removed_in="2.0", current_version=__version__,
+            details="The connection module is deprecated.")
 def raise_unsupported_auth_mechanism(mechanism):
     msg = "Auth mechanism '{}' not supported."
     raise ValueError(msg.format(mechanism))
 
 
+@deprecated(deprecated_in="1.3", removed_in="2.0", current_version=__version__,
+            details="The connection module is deprecated.")
 class DBClientConnector(object):
 
     def __init__(self, host_config, **kwargs):

signac/common/crypt.py

@@ -4,6 +4,8 @@
 import base64
 
 from . import six
+from deprecation import deprecated
+from ..version import __version__
 
 try:
     from passlib.context import CryptContext
@@ -27,7 +29,13 @@ def get_keyring():
         "Return the system user keyring."
         return keyring.get_keyring()
 
+"""
+THIS MODULE IS DEPRECATED!
+"""
 
+
+@deprecated(deprecated_in="1.3", removed_in="2.0", current_version=__version__,
+            details="The crypt module is deprecated.")
 class SimpleKeyring(object):
     """Simple in-memory keyring for caching."""
 
@@ -65,6 +73,8 @@ def setdefault(self, key, value):
         return self._decode(self._cache.setdefault(key, self._encode(value)))
 
 
+@deprecated(deprecated_in="1.3", removed_in="2.0", current_version=__version__,
+            details="The crypt module is deprecated.")
 def parse_pwhash(pwhash):
     "Extract hash configuration from hash string."
     if get_crypt_context().identify(pwhash) == 'bcrypt':

signac/common/host.py

@@ -5,6 +5,8 @@
 import warnings
 import getpass
 
+from deprecation import deprecated
+from ..version import __version__
 from ..core import json
 from .config import load_config
 from .errors import ConfigError, AuthenticationError
@@ -18,7 +20,13 @@
 SESSION_PASSWORD_HASH_CACHE = SimpleKeyring()
 SESSION_USERNAME_CACHE = dict()
 
+"""
+THIS MODULE IS DEPRECATED!
+"""
 
+
+@deprecated(deprecated_in="1.3", removed_in="2.0", current_version=__version__,
+            details="The host module is deprecated.")
 def get_default_host(config=None):
     if config is None:
         config = load_config()
@@ -38,6 +46,8 @@ def _get_host_config(hostname, config):
         raise ConfigError("Host '{}' not configured.".format(hostname))
 
 
+@deprecated(deprecated_in="1.3", removed_in="2.0", current_version=__version__,
+            details="The host module is deprecated.")
 def get_host_config(hostname=None, config=None):
     if config is None:
         config = load_config()
@@ -50,6 +60,8 @@ def _host_id(hostcfg):
     return json.dumps(hostcfg, sort_keys=True)
 
 
+@deprecated(deprecated_in="1.3", removed_in="2.0", current_version=__version__,
+            details="The host module is deprecated.")
 def make_uri(hostcfg):
     ret = hostcfg['url']
     if ret.startswith('mongodb://'):
@@ -116,6 +128,8 @@ def default():
     return _get_cached_credentials(hostcfg, default)
 
 
+@deprecated(deprecated_in="1.3", removed_in="2.0", current_version=__version__,
+            details="The host module is deprecated.")
 def get_credentials(hostcfg, ask=True):
     if ask:
         return _get_credentials(hostcfg)
@@ -135,6 +149,8 @@ def _input(prompt, default=''):
         return default
 
 
+@deprecated(deprecated_in="1.3", removed_in="2.0", current_version=__version__,
+            details="The host module is deprecated.")
 def check_credentials(hostcfg):
     from pymongo.uri_parser import parse_uri
     auth_m = hostcfg.get('auth_mechanism', 'none')
@@ -156,17 +172,23 @@ def check_credentials(hostcfg):
     return hostcfg
 
 
+@deprecated(deprecated_in="1.3", removed_in="2.0", current_version=__version__,
+            details="The host module is deprecated.")
 def get_connector(hostcfg, **kwargs):
     return DBClientConnector(hostcfg, **kwargs)
 
 
+@deprecated(deprecated_in="1.3", removed_in="2.0", current_version=__version__,
+            details="The host module is deprecated.")
 def get_client(hostcfg, **kwargs):
     connector = get_connector(hostcfg, **kwargs)
     connector.connect()
     connector.authenticate()
     return connector.client
 
 
+@deprecated(deprecated_in="1.3", removed_in="2.0", current_version=__version__,
+            details="The host module is deprecated.")
 def get_database(name, hostname=None, config=None, **kwargs):
     if hostname is None:
         hostname = get_default_host(config)

signac/contrib/filesystems.py

@@ -11,6 +11,8 @@
 
 from ..common import six
 from ..db import get_database
+from ..version import __version__
+from deprecation import deprecated
 
 try:
     import pymongo
@@ -27,12 +29,18 @@
 GRIDFS_LARGE_FILE_WARNING_THRSHLD = int(1e9)  # 1GB
 FILESYSTEM_REGISTRY = dict()
 
+"""
+THIS MODULE IS DEPRECATED!
+"""
+
 
 def _register_fs_class(fs):
     "Register a file system handler in the module's registry."
     FILESYSTEM_REGISTRY[fs.name] = fs
 
 
+@deprecated(deprecated_in="1.3", removed_in="2.0", current_version=__version__,
+            details="The filesystems module is deprecated.")
 class LocalFS(object):
     """A file system handler for the local file system.
 
@@ -193,7 +201,8 @@ def get(self, _id, mode='r'):
                 raise ValueError(mode)
     _register_fs_class(GridFS)
 
-
+@deprecated(deprecated_in="1.3", removed_in="2.0", current_version=__version__,
+            details="The filesystems module is deprecated.")
 def filesystems_from_config(fs_config):
     """Generate file system handlers from a configuration.
 
@@ -236,7 +245,8 @@ def filesystems_from_config(fs_config):
         else:
             yield fs_class(args)
 
-
+@deprecated(deprecated_in="1.3", removed_in="2.0", current_version=__version__,
+            details="The filesystems module is deprecated.")
 def filesystems_from_configs(fs_configs):
     """Generate file system handlers.