Scheduled monthly dependency update for May (#893)

* Update pymdown-extensions from 7.1 to 9.4 * Update mkdocs-material from 7.0.6 to 8.2.12 * Update mkdocstrings from 0.12.0 to 0.18.1 * Update black from 19.10b0 to 22.3.0 * Update wheel from 0.34.2 to 0.37.1 * Update alembic from 1.4.2 to 1.7.7 * Update sqlalchemy from 1.3.18 to 1.4.36 * Update pyyaml from 5.4.1 to 6.0 * Update psycopg2-binary from 2.8.5 to 2.9.3 * Update python-dateutil from 2.8.1 to 2.8.2 * Update boto3 from 1.14.45 to 1.22.4 * Update click from 7.1.2 to 8.1.3 * Update inflection from 0.5.0 to 0.5.1 * Update numpy from 1.21.1 to 1.22.3 * Update s3fs from 0.4.2 to 2022.3.0 * Update wrapt from 1.13.3 to 1.14.0 * Update pebble from 4.5.3 to 4.6.3 * Update graphviz from 0.14 to 0.20 * Update requests from 2.24.0 to 2.27.1 * Update coloredlogs from 14.0 to 15.0.1 * Update scipy from 1.5.0 to 1.8.0 * Update scikit-learn from 0.23.1 to 1.0.2 * Update matplotlib from 3.3.4 to 3.5.1 * Update pandas from 1.0.5 to 1.4.2 * Update seaborn from 0.10.1 to 0.11.2 * Update csvkit from 1.0.5 to 1.0.7 * Update factory_boy from 2.12.0 to 3.2.1 * Update pytest-cov from 2.10.0 to 3.0.0 * Update moto from 1.3.14 to 3.1.7 * Update fakeredis from 1.4.1 to 1.7.1 * Update hypothesis from 5.19.0 to 6.46.1 * Update flake8 from 3.8.3 to 4.0.1 * Update codecov from 2.1.7 to 2.1.12 * Update tox from 3.16.1 to 3.25.0 * Don't upgrade sqlalchemy, resolve s3fs * Fix type on as-of-date index * Add location to mocked buckets * Fix type in log * Change print to logs * Downgrade pandas to be compatible with sqlalchemy * Remove support for Python 7 * Add support for python 3.10 * Quote python versions * Require pandas 1.3.5 * Update pymdown-extensions from 7.1 to 9.4 * Update mkdocs-material from 7.0.6 to 8.2.12 * Update mkdocstrings from 0.12.0 to 0.18.1 * Update black from 19.10b0 to 22.3.0 * Update wheel from 0.34.2 to 0.37.1 * Update alembic from 1.4.2 to 1.7.7 * Update sqlalchemy from 1.3.18 to 1.4.36 * Update pyyaml from 5.4.1 to 6.0 * Update psycopg2-binary from 2.8.5 to 2.9.3 * Update python-dateutil from 2.8.1 to 2.8.2 * Update boto3 from 1.14.45 to 1.22.4 * Update click from 7.1.2 to 8.1.3 * Update inflection from 0.5.0 to 0.5.1 * Update numpy from 1.21.1 to 1.22.3 * Update s3fs from 0.4.2 to 2022.3.0 * Update wrapt from 1.13.3 to 1.14.0 * Update pebble from 4.5.3 to 4.6.3 * Update graphviz from 0.14 to 0.20 * Update requests from 2.24.0 to 2.27.1 * Update coloredlogs from 14.0 to 15.0.1 * Update scipy from 1.5.0 to 1.8.0 * Update scikit-learn from 0.23.1 to 1.0.2 * Update matplotlib from 3.3.4 to 3.5.1 * Update pandas from 1.0.5 to 1.4.2 * Update seaborn from 0.10.1 to 0.11.2 * Update csvkit from 1.0.5 to 1.0.7 * Update factory_boy from 2.12.0 to 3.2.1 * Update pytest-cov from 2.10.0 to 3.0.0 * Update moto from 1.3.14 to 3.1.7 * Update fakeredis from 1.4.1 to 1.7.1 * Update hypothesis from 5.19.0 to 6.46.1 * Update flake8 from 3.8.3 to 4.0.1 * Update codecov from 2.1.7 to 2.1.12 * Update tox from 3.16.1 to 3.25.0 * Don't upgrade sqlalchemy, resolve s3fs * Fix type on as-of-date index * Add location to mocked buckets * Fix type in log * Change print to logs * Downgrade pandas to be compatible with sqlalchemy * Remove support for Python 7 * Add support for python 3.10 * Quote python versions * Require pandas 1.3.5 * Upgrade pytest to be compatible w python 3.10 * Use f-string for logs * Tell pyup to ignore s3fs, sqlalchemy, pandas * Catch when all evaluations are NaN * One more spot to update python version * Update src/tests/catwalk_tests/test_evaluation.py Co-authored-by: ecsalomon <ecsalomon@gmail.com> Co-authored-by: Kit Rodolfa <shaycrk@gmail.com>
dssg · May 20, 2022 · 7b52958 · 7b52958
1 parent 65a83a2
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diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -8,10 +8,10 @@ jobs:
     runs-on: ubuntu-18.04
     steps:
     - uses: actions/checkout@master
-    - name: Set up Python 3.7
+    - name: Set up Python 3.8
       uses: actions/setup-python@v1
       with:
-        python-version: 3.7
+        python-version: 3.8
     - name: Install pypa/build
       run: >-
         python -m

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -22,7 +22,7 @@ jobs:
           --health-retries 5
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ['3.8', '3.9', '3.10']
 
     steps:
     - uses: actions/checkout@v2

diff --git a/.travis.yml b/.travis.yml
@@ -1,6 +1,6 @@
 dist: bionic
 language: python
-python: ["3.6", "3.7"]
+python: ["3.8", "3.9", "3.10"]
 addons:
   postgresql: '11'
   apt:

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.7-slim AS development
+FROM python:3.8-slim AS development
 
 LABEL creator="Center for Data Science and Public Policy (DSaPP)" \
         maintainer="Adolfo De Unánue <adolfo@cmu.edu>" \
@@ -60,7 +60,7 @@ RUN pip install -e .
 
 ENTRYPOINT [ "bash" ]
 
-FROM python:3.7-slim AS master
+FROM python:3.8-slim AS master
 
 LABEL triage.version="master"
 

diff --git a/README.md b/README.md
@@ -25,7 +25,7 @@ Triage is designed to:
 
 To install Triage, you need:
 
-- Python 3.7+
+- Python 3.8+
 - A PostgreSQL 9.6+ database with your source data (events,
   geographical data, etc) loaded.
   - **NOTE**: If your database is PostgreSQL 11+ you will get some

diff --git a/docs/sources/dirtyduck/dirty_duckling.md b/docs/sources/dirtyduck/dirty_duckling.md
@@ -242,7 +242,7 @@ triage experiment experiments/dirty-duckling.yaml
 ```
 That's it! If you see this message in your screen:
 
-     2020-08-20 16:56:56 - SUCCESS Training, testing and evaluatiog models completed
+     2020-08-20 16:56:56 - SUCCESS Training, testing and evaluating models completed
      2020-08-20 16:56:56 - SUCCESS All matrices that were supposed to be build were built. Awesome!
      2020-08-20 16:56:56 - SUCCESS All models that were supposed to be trained were trained. Awesome!
      2020-08-20 16:56:56 - SUCCESS Experiment (a336de4800cec8964569d051dc56f85d) ran through completion

diff --git a/docs/sources/experiments/running.md b/docs/sources/experiments/running.md
@@ -4,7 +4,7 @@
 
 To use a Triage experiment, you first need:
 
-- Python 3.7+
+- Python 3.8+
 - A PostgreSQL (v9.6+) database with your source data (events, geographical data, etc) loaded.
 - Ample space on an available disk (or S3) to store the needed matrices and models for your experiment
 - An experiment definition (see [Experiment configuration](experiment-config.md))

diff --git a/docs/sources/index.md b/docs/sources/index.md
@@ -25,7 +25,7 @@ Triage is designed to:
 
 To install Triage, you need:
 
-- Python 3.7+
+- Python 3.8+
 - A PostgreSQL 9.6+ database with your source data (events,
   geographical data, etc) loaded.
   - **NOTE**: If your database is PostgreSQL 11+ you will get some

diff --git a/docs/sources/quickstart.md b/docs/sources/quickstart.md
@@ -137,7 +137,7 @@ defaults for others. The primary parameters to specify (for now) are:
    - `entity_id`: each `entity_id` affected by an event within the amount of time specified by `label_timespan` after a given `as_of_date`
    - `outcome`: a binary variable representing the events that happened to each entity, within the period specified by that `as_of_date` and `label_timespan`
 
-   The query is parameterized over `as_of_date`, and `label_timespan`. These parameters are passed to your query as named keywords using the Python's [`str.format()`](https://docs.python.org/3.7/library/stdtypes.html#str.format) method. You can use them in your query by surrounding their keywords with curly braces (as in the example below).
+   The query is parameterized over `as_of_date`, and `label_timespan`. These parameters are passed to your query as named keywords using the Python's [`str.format()`](https://docs.python.org/3.8/library/stdtypes.html#str.format) method. You can use them in your query by surrounding their keywords with curly braces (as in the example below).
 
    See our
    [guide to Labels](https://dssg.github.io/triage/experiments/cohort-labels/) for a more in-depth discussion of this topic.

diff --git a/requirement/dev.txt b/requirement/dev.txt
@@ -1,7 +1,7 @@
 -r include/build.txt
 bumpversion==0.6.0
 mkdocs==1.3.0
-pymdown-extensions==7.1
-mkdocs-material==7.0.6
-mkdocstrings==0.12.0
-black==19.10b0
+pymdown-extensions==9.4
+mkdocs-material==8.2.12
+mkdocstrings==0.18.1
+black==22.3.0
diff --git a/requirement/include/build.txt b/requirement/include/build.txt
@@ -1 +1 @@
-wheel==0.34.2
+wheel==0.37.1
diff --git a/requirement/include/lint.txt b/requirement/include/lint.txt
@@ -1 +1 @@
-flake8==3.8.3
+flake8==4.0.1
diff --git a/requirement/include/test-management.txt b/requirement/include/test-management.txt
@@ -1,3 +1,3 @@
-codecov==2.1.7
+codecov==2.1.12
 coverage>=4.4
-tox==3.16.1
+tox==3.25.0
diff --git a/requirement/main.txt b/requirement/main.txt
@@ -1,31 +1,31 @@
-alembic==1.4.2
-SQLAlchemy==1.3.18
-PyYAML==5.4.1
-psycopg2-binary==2.8.5
-python-dateutil==2.8.1
-boto3==1.14.45
-click==7.1.2
-inflection==0.5.0
-numpy==1.21.1
+alembic==1.7.7
+SQLAlchemy==1.3.18 # pyup: ignore
+PyYAML==6.0
+psycopg2-binary==2.9.3
+python-dateutil==2.8.2
+boto3==1.22.4
+click==8.1.3
+inflection==0.5.1
+numpy==1.22.3
 sqlalchemy-postgres-copy==0.5.0
 retrying==1.3.3
 Dickens==1.0.1
 signalled-timeout==1.0.0
-s3fs==0.4.2
-wrapt==1.13.3
+wrapt==1.14.0
 argcmdr==0.7.0
 sqlparse==0.4.2
-pebble==4.5.3
+pebble==4.6.3
 adjustText==0.7.3
-graphviz==0.14
-requests==2.24.0
-coloredlogs==14.0
+graphviz==0.20
+requests==2.27.1
+coloredlogs==15.0.1
 verboselogs==1.7
-scipy==1.5.0
-scikit-learn==0.23.1
-matplotlib==3.3.4
-pandas==1.0.5
-seaborn==0.10.1
+s3fs==0.4.2 # pyup: ignore
+scipy==1.8.0
+scikit-learn==1.0.2
+matplotlib==3.5.1
+pandas==1.3.5 # pyup: ignore
+seaborn==0.11.2
 ohio==0.5.0
 
 

diff --git a/requirement/test.txt b/requirement/test.txt
@@ -1,11 +1,11 @@
 -r include/lint.txt
 -r include/test-management.txt
 parsedatetime==2.6
-csvkit==1.0.5
-factory_boy==2.12.0
+csvkit==1.0.7
+factory_boy==3.2.1
 testing.postgresql==1.3.0
-pytest==5.4.3 #<4.0.0 # pyup: ignore
-pytest-cov==2.10.0
-moto==1.3.14
-fakeredis==1.4.1
-hypothesis==5.19.0
+pytest==6.2.5 #<4.0.0 # pyup: ignore
+pytest-cov==3.0.0
+moto==3.1.7
+fakeredis==1.7.1
+hypothesis==6.46.1
diff --git a/setup.py b/setup.py
@@ -7,15 +7,15 @@
 
 ROOT_PATH = Path(__file__).parent
 
-LICENSE_PATH = ROOT_PATH / 'LICENSE'
+LICENSE_PATH = ROOT_PATH / "LICENSE"
 
-README_PATH = ROOT_PATH / 'README.md'
+README_PATH = ROOT_PATH / "README.md"
 
-REQUIREMENTS_PATH = ROOT_PATH / 'requirement' / 'main.txt'
+REQUIREMENTS_PATH = ROOT_PATH / "requirement" / "main.txt"
 
-REQUIREMENTS_TEST_PATH = ROOT_PATH / 'requirement' / 'test.txt'
+REQUIREMENTS_TEST_PATH = ROOT_PATH / "requirement" / "test.txt"
 
-REQUIREMENTS_RQ_PATH = ROOT_PATH / 'requirement' / 'extras-rq.txt'
+REQUIREMENTS_RQ_PATH = ROOT_PATH / "requirement" / "extras-rq.txt"
 
 
 def stream_requirements(fd):
@@ -25,8 +25,8 @@ def stream_requirements(fd):
 
     """
     for line in fd:
-        cleaned = re.sub(r'#.*$', '', line).strip()
-        if cleaned and not cleaned.startswith('-r'):
+        cleaned = re.sub(r"#.*$", "", line).strip()
+        if cleaned and not cleaned.startswith("-r"):
             yield cleaned
 
 
@@ -43,40 +43,41 @@ def stream_requirements(fd):
 
 
 setup(
-    name='triage',
-    version='5.1.1',
+    name="triage",
+    version="5.1.1",
     description="Risk modeling and prediction",
     long_description=README_PATH.read_text(),
     long_description_content_type="text/markdown",
     author="Center for Data Science and Public Policy",
-    author_email='datascifellows@gmail.com',
+    author_email="datascifellows@gmail.com",
     url="https://dssg.github.io/triage/",
     project_urls={
         "Documentation": "https://dssg.github.io/triage/",
         "Source Code": "https://github.com/dssg/triage",
-        "Tutorial": "https://dssg.github.io/triage/dirtyduck/"
+        "Tutorial": "https://dssg.github.io/triage/dirtyduck/",
     },
-    packages=find_packages('src', exclude=['tests', 'tests.*']),
-    package_dir={'': 'src'},
+    packages=find_packages("src", exclude=["tests", "tests.*"]),
+    package_dir={"": "src"},
     include_package_data=True,
     install_requires=REQUIREMENTS,
     entry_points={
-        'console_scripts': ['triage = triage.cli:execute'],
+        "console_scripts": ["triage = triage.cli:execute"],
     },
-    extras_require={'rq': RQ_REQUIREMENTS},
+    extras_require={"rq": RQ_REQUIREMENTS},
     license="MIT License",
     zip_safe=False,
-    keywords='triage',
+    keywords="triage",
     classifiers=[
-        'Development Status :: 2 - Pre-Alpha',
-        'Intended Audience :: Developers',
-        'License :: OSI Approved :: MIT License',
-        'Natural Language :: English',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
+        "Development Status :: 2 - Pre-Alpha",
+        "Intended Audience :: Developers",
+        "License :: OSI Approved :: MIT License",
+        "Natural Language :: English",
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
     ],
-    python_requires='>=3.6',
-    test_suite='tests',
-    tests_require=REQUIREMENTS_TEST
+    python_requires=">=3.8",
+    test_suite="tests",
+    tests_require=REQUIREMENTS_TEST,
 )
diff --git a/src/tests/architect_tests/test_builders.py b/src/tests/architect_tests/test_builders.py
@@ -3,6 +3,8 @@
 
 import pandas as pd
 import testing.postgresql
+from unittest.mock import Mock
+
 from triage import create_engine
 from contextlib import contextmanager
 
@@ -421,11 +423,11 @@ def test_load_features_data():
         cols = ["entity_id", "as_of_date"] + features[i]
         temp_df = pd.DataFrame(table, columns=cols)
         temp_df["as_of_date"] = convert_string_column_to_date(temp_df["as_of_date"])
-        features_dfs.append(
-            ids_dates.merge(
-                right=temp_df, how="left", on=["entity_id", "as_of_date"]
-            ).set_index(["entity_id", "as_of_date"])
+        merged_df = ids_dates.merge(
+            right=temp_df, how="left", on=["entity_id", "as_of_date"]
         )
+        merged_df["as_of_date"] = pd.to_datetime(merged_df["as_of_date"])
+        features_dfs.append(merged_df.set_index(["entity_id", "as_of_date"]))
 
     # create an engine and generate a table with fake feature data
     with testing.postgresql.Postgresql() as postgresql: