Remove python 3.6 support (#78)

* Remove python 3.6 support

* Remove easydict and pin requirements

* Fix typo

* Set python minor version on travis

* Also remove local db in delete script

.pre-commit-config.yaml

@@ -1,17 +1,14 @@
 repos:
-- repo: https://github.com/pre-commit/mirrors-isort
-  rev: 'v4.3.16'
-  hooks:
-    - id: isort
-      additional_dependencies: ['future-fstrings==1.0.0', 'isort[pyproject]']
-- repo: https://github.com/ambv/black
-  rev: stable
-  hooks:
-  - id: black
-    language_version: python3.6
-    additional_dependencies: ['future-fstrings==1.0.0']
--  repo: https://github.com/pre-commit/mirrors-mypy
-   rev: 'v0.730'
-   hooks:
-   - id: mypy
-     additional_dependencies: ['future-fstrings==1.0.0']
+  - repo: https://github.com/pre-commit/mirrors-isort
+    rev: "v5.10.1"
+    hooks:
+      - id: isort
+  - repo: https://github.com/ambv/black
+    rev: stable
+    hooks:
+      - id: black
+        language_version: python3.7
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v0.960"
+    hooks:
+      - id: mypy

.travis.yml

@@ -1,11 +1,9 @@
 sudo: required
 language: python
 python:
-  #  - "3.5"
-  - "3.6"
-  - "3.7"
+  - "3.7.13"
   - "3.8"
-os:  linux
+os: linux
 dist: xenial
 cache: pip
 services:

.vscode/settings.json

@@ -4,5 +4,6 @@
     "python.testing.unittestEnabled": false,
     "python.testing.nosetestsEnabled": false,
     "python.testing.pytestEnabled": true,
-    "restructuredtext.confPath": "${workspaceFolder}/.tox/py36/lib/python3.6/site-packages/importlib_resources/docs"
+    "restructuredtext.confPath": "${workspaceFolder}/.tox/py36/lib/python3.7/site-packages/importlib_resources/docs",
+    "esbonio.sphinx.confDir": "${workspaceFolder}/.tox/py36/lib/python3.7/site-packages/importlib_resources/docs"
 }

Dockerfile

@@ -23,8 +23,8 @@ RUN groupadd --gid $USER_GID $USERNAME \
 # Install git, process tools, lsb-release (common in install instructions for CLIs)
 RUN apt -y install git procps lsb-release ffmpeg vim exuberant-ctags zsh wget
 
-# Install any missing dependencies for enhanced language service
-RUN apt install -y libicu[0-9][0-9]
+# # Install any missing dependencies for enhanced language service
+# RUN apt install -y libicu[0-9][0-9]
 
 # Clean up
 RUN apt-get autoremove -y \
@@ -46,7 +46,7 @@ RUN mkdir -p ${HOME}/.ssh \
 WORKDIR ${HOME}/workspace
 
 # Install Python dependencies from requirements.txt if it exists
-RUN conda create -n env python=3.6
+RUN conda create -n env python=3.7
 RUN echo "source activate env" > ~/.bashrc
 ENV PATH /opt/conda/envs/env/bin:$PATH
 RUN conda install virtualenv

README.rst

@@ -83,7 +83,7 @@ Alternatively, you can use conda to set up your local development environment.
 
 ::
 
-  $ conda create -n incense-dev python=3.6
+  $ conda create -n incense-dev python=3.7
   $ conda activate incense-dev
   # virtualenv is required for the precommit environments.
   $ conda install virtualenv

binder/environment.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - anaconda
 dependencies:
-  - python=3.6
+  - python=3.7
   - numpy
   - matplotlib
   - pandas
@@ -12,5 +12,5 @@ dependencies:
   - mongodb
   - seaborn
   - pip:
-    - git+https://github.com/IDSIA/sacred.git
-    - incense
+      - git+https://github.com/IDSIA/sacred.git
+      - incense

delete_db.py

@@ -1,14 +1,18 @@
 import os
+import shutil
 from pathlib import Path
 
 from dotenv import load_dotenv
-from pymongo import MongoClient
+from pymongo.mongo_client import MongoClient
 
 env_path = Path(".") / "infrastructure" / "sacred_setup" / ".env"
 load_dotenv(dotenv_path=env_path)
 
 DB_NAME = os.environ["MONGO_DATABASE"]
 
-client = MongoClient(host="mongo")
+client: MongoClient = MongoClient(host="mongo")
 client.drop_database(DB_NAME)
+
+shutil.rmtree(Path("~/data/incense_test/").expanduser(), ignore_errors=True)
+
 print(f"Database {DB_NAME} successfully deleted.")

incense/artifact.py

@@ -1,4 +1,3 @@
-# -*- coding: future_fstrings -*-
 import os
 import pickle
 import warnings

incense/experiment.py

@@ -1,13 +1,13 @@
-# -*- coding: future_fstrings -*-
 import json
 from pathlib import Path
 from typing import *
 
 import jsonpickle
 import pandas as pd
-from incense.artifact import Artifact, content_type_to_artifact_cls
 from pyrsistent import freeze, thaw
 
+from incense.artifact import Artifact, content_type_to_artifact_cls
+
 
 class Experiment:
     def __init__(self, id_, database, grid_filesystem, data, artifact_links, loader):

incense/experiment_loader.py

@@ -1,13 +1,12 @@
-# -*- coding: future_fstrings -*-
 import importlib
 import numbers
-from functools import _lru_cache_wrapper, lru_cache
+from functools import lru_cache
 from pathlib import Path
 from typing import *
 
 import gridfs
-import pymongo
-from pymongo import MongoClient
+from pymongo import DESCENDING
+from pymongo.mongo_client import MongoClient
 
 from .experiment import Experiment, FileSystemExperiment
 from .query_set import QuerySet
@@ -19,7 +18,7 @@ class ExperimentLoader:
     """Loads artifacts related to experiments."""
 
     def __init__(self, mongo_uri=None, db_name="sacred", unpickle: bool = True):
-        client = MongoClient(mongo_uri)
+        client: MongoClient = MongoClient(mongo_uri)
         self._database = client[db_name]
         self._runs = self._database.runs
         self._grid_filesystem = gridfs.GridFS(self._database)
@@ -140,7 +139,7 @@ def find_latest(self, n: int = 1, attr: str = "start_time") -> Union[Experiment,
         Returns:
             Either the latest experiment or the set of latest experiments in case more than one were requested.
         """
-        cursor = self._runs.find().sort(attr, pymongo.DESCENDING).limit(n)
+        cursor = self._runs.find().sort(attr, DESCENDING).limit(n)
         experiments = [self._make_experiment(experiment) for experiment in cursor]
         if len(experiments) == 1:
             return experiments[0]
@@ -189,6 +188,8 @@ def _search_collection(self, key, value):
             cursor = self._runs.find({key: {"$regex": rf"{value}"}})
         elif isinstance(value, numbers.Real):
             cursor = self._runs.find({key: value})
+        else:
+            raise ValueError(f"Search value should be either string or number, but was {value}")
         return cursor
 
 

incense/query_set.py

@@ -1,4 +1,3 @@
-# -*- coding: future_fstrings -*-
 from collections import OrderedDict, UserList, defaultdict
 from concurrent.futures import ThreadPoolExecutor
 from copy import copy
@@ -31,8 +30,8 @@ def project(
             values in the experiment model can be used inplace of a path. This is useful for summarizing metrics.
         rename: The renaming strategy used to create the column names. Either "last" to take the last element in each
                 path as a column name or None to use the complete paths as column names.
-        on_missing: {"raise", "ignore"} Whether to raise an error when missing value is encountered or replace it with 
-                    a missing value. 
+        on_missing: {"raise", "ignore"} Whether to raise an error when missing value is encountered or replace it with
+                    a missing value.
 
         Returns
         -------

incense/utils.py

@@ -1,4 +1,3 @@
-# -*- coding: future_fstrings -*-
 from functools import reduce
 from operator import and_, or_
 from typing import *

mypy.ini

@@ -1,5 +1,5 @@
 [mypy]
-python_version = 3.6
+python_version = 3.7
 ignore_missing_imports = True
 
 [mypy-versioneer.py]

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.black]
 line-length = 120
-target-version = ['py36']
+target-version = ['py37']
 include = '\.pyi?$'
 exclude = '''
 (

requirements-dev.txt

@@ -1,16 +1,14 @@
 -r requirements.txt
-pytest
-pytest-cov
-codecov
-tensorflow==2.5.3
-python-dotenv
-scikit-learn
-jupyterlab
-seaborn
-pre-commit
-tokenize-rt==2.2.0
-pylint
-black
-doc8
-rope
-mypy==0.780
+pytest==7.1.2
+pytest-cov==3.0.0
+codecov==2.1.12
+tensorflow==2.9.1
+python-dotenv==0.20.0
+scikit-learn==1.0.2
+jupyterlab==3.4.2
+seaborn==0.11.2
+pre-commit==2.19.0
+black==22.3.0
+doc8==0.11.2
+rope==1.1.1
+mypy==0.960

requirements.txt

@@ -1,7 +1,6 @@
-sacred>=0.8
-pandas>=0.23
-pymongo>=3.7
-easydict>=1.9
-ipython>=7.2
-future-fstrings==1.0.0
+sacred==0.8.2
+pandas==1.3.5
+pymongo==4.1.1
+ipython==7.33.0
+pyrsistent==0.18.1
 attrs==19.3.0

setup.py

@@ -29,15 +29,11 @@
         "jupyterlab>=1.0",
         "pymongo>=3.7",
         "pyrsistent>=0.15.2",
-        "future-fstrings==1.0.0",
-        "tokenize-rt==2.2.0",
     ],
     include_package_data=True,
     classifiers=[
         "Development Status :: 3 - Alpha",
         "Intended Audience :: Science/Research",
-        "Programming Language :: Python :: 3.5",
-        "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
     ],

tests/example_experiment/conduct.py

@@ -1,4 +1,3 @@
-# -*- coding: future_fstrings -*-
 import os
 from pathlib import Path
 

tests/test_artifact.py

@@ -1,15 +1,15 @@
-# -*- coding: future_fstrings -*-
 import imghdr
 import os
 import pickle
 
 import IPython
 import pandas as pd
 import pytest
-from incense import artifact
 from IPython.display import HTML
 from pytest import raises
 
+from incense import artifact
+
 
 def test_repr(loader):
     exp = loader.find_by_id(3)

tests/test_experiment.py

@@ -1,4 +1,3 @@
-# -*- coding: future_fstrings -*-
 import collections.abc
 from datetime import datetime
 from fractions import Fraction

tests/test_experiment_loader.py

@@ -1,12 +1,12 @@
-# -*- coding: future_fstrings -*-
 from pathlib import Path
 
 import pytest
-from incense.experiment import Experiment, FileSystemExperiment
-from incense.experiment_loader import FileSystemExperimentLoader
 from pytest import raises
 from sacred import Experiment as SacredExperiment
 
+from incense.experiment import Experiment, FileSystemExperiment
+from incense.experiment_loader import FileSystemExperimentLoader
+
 
 def test_find_by_id(loader):
     exp = loader.find_by_id(1)

tests/test_projector.py

@@ -1,4 +1,3 @@
-# -*- coding: future_fstrings -*-
 import numpy as np
 import pandas as pd
 from pandas.testing import assert_frame_equal

tests/test_set_save.py

@@ -1,4 +1,3 @@
-# -*- coding: future_fstrings -*-
 import os
 
 

tox.ini

@@ -1,9 +1,8 @@
 [tox]
-envlist = py35, py36, py37, py38, mypy
+envlist = py37, py38, mypy
 
 [travis]
 python =
-  3.6: py36
   3.7: py37
   3.8: py38, mypy
 
@@ -20,4 +19,4 @@ basepython = python3.8
 commands =
     mypy --package incense
 deps =
-    mypy==0.780
+    mypy==0.960

versioneer.py

@@ -277,18 +277,14 @@
 
 from __future__ import print_function
 
+import configparser
 import errno
 import json
 import os
 import re
 import subprocess
 import sys
 
-try:
-    import configparser
-except ImportError:
-    import ConfigParser as configparser
-
 
 class VersioneerConfig:
     """Container for Versioneer configuration parameters."""