Merge pull request #22 from MiraGeoscience/release/0.1.5

Release/0.1.5

Author: andrewg-mira

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"

.github/workflows/issue_to_jira.yml

@@ -12,14 +12,14 @@ jobs:
 
     steps:
     - name: JIRA Login
-      uses: atlassian/gajira-login@v2.0.0
+      uses: atlassian/gajira-login@v3.0.1
       env:
         JIRA_BASE_URL: ${{ secrets.JIRA_BASE_URL }}
         JIRA_USER_EMAIL: ${{ secrets.JIRA_USER_EMAIL }}
         JIRA_API_TOKEN: ${{ secrets.JIRA_API_TOKEN }}
     - name: Jira Create issue
       id: create_jira_issue
-      uses: atlassian/gajira-create@v2.0.1
+      uses: atlassian/gajira-create@v3.0.1
       with:
         project: GEOPY
         issuetype: Story
@@ -28,7 +28,7 @@ jobs:
         # Additional fields in JSON format
         fields: '{"components": [{"name": "param-sweeps"}]}'
     - name: Post JIRA link
-      uses: peter-evans/create-or-update-comment@v1
+      uses: peter-evans/create-or-update-comment@v2
       with:
         # The number of the issue or pull request in which to create a comment.
         issue-number: ${{ github.event.issue.number }}

.github/workflows/pytest-unix-os.yml

@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python_ver: [3.7, 3.8, 3.9]
+        python_ver: ['3.8', '3.9', '3.10']
     defaults:
       run:
         shell: bash
@@ -32,9 +32,9 @@ jobs:
       POETRY_VIRTUALENVS_CREATE: true
       POETRY_VIRTUALENVS_IN_PROJECT: true
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python version
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python_ver }}
     - name: Get full Python version
@@ -45,7 +45,7 @@ jobs:
         curl -sSL https://install.python-poetry.org | POETRY_HOME=$HOME/.poetry python -
         echo "$HOME/.poetry/bin" >> $GITHUB_PATH
     - name: Set up cache
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache
       env:
         # Increase this value to reset cache if poetry.lock has not changed

.github/workflows/pytest-windows.yml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python_ver: [3.7, 3.8, 3.9]
+        python_ver: ['3.8', '3.9', '3.10']
     defaults:
       run:
         shell: bash
@@ -31,9 +31,9 @@ jobs:
       POETRY_VIRTUALENVS_CREATE: true
       POETRY_VIRTUALENVS_IN_PROJECT: true
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python version
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python_ver }}
     - name: Get full Python version
@@ -44,7 +44,7 @@ jobs:
         curl -sSL https://install.python-poetry.org | POETRY_HOME=$HOME/.poetry python -
         echo "$HOME/.poetry/bin" >> $GITHUB_PATH
     - name: Set up cache
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache
       env:
         # Increase this value to reset cache if poetry.lock has not changed
@@ -60,7 +60,7 @@ jobs:
     - name: pytest
       run: poetry run pytest --cov-report=xml --cov=param_sweeps --cov-branch --cov-fail-under=85
     - name: Codecov
-      if: ${{ success() && matrix.python_ver == '3.7' }}
-      uses: codecov/codecov-action@v1
+      if: ${{ success() && matrix.python_ver == '3.10' }}
+      uses: codecov/codecov-action@v3
       with:
         name: GitHub

.github/workflows/static-analysis.yml

@@ -24,11 +24,11 @@ jobs:
       POETRY_VIRTUALENVS_CREATE: true
       POETRY_VIRTUALENVS_IN_PROJECT: true
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python version
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.7
+        python-version: 3.9
     - name: Get full Python version
       id: full-python-version
       shell: bash
@@ -38,7 +38,7 @@ jobs:
         curl -sSL https://install.python-poetry.org | POETRY_HOME=$HOME/.poetry python -
         echo "$HOME/.poetry/bin" >> $GITHUB_PATH
     - name: Set up cache
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache
       env:
         # Increase this value to reset cache if poetry.lock has not changed

.pre-commit-config.yaml

@@ -10,19 +10,13 @@ ci:
 
 repos:
 -   repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 23.1.0
     hooks:
     -   id: black
         types: [text]
         types_or: [python, pyi]
--   repo: https://github.com/asottile/seed-isort-config
-    rev: v2.2.0
-    hooks:
-    -   id: seed-isort-config
-        types: [text]
-        types_or: [python, pyi]
 -   repo: https://github.com/PyCQA/isort
-    rev: 5.11.4
+    rev: 5.12.0
     hooks:
     -   id: isort
         additional_dependencies: [toml] # to read config from pyproject.toml
@@ -44,11 +38,11 @@ repos:
     rev: v3.3.1
     hooks:
     -   id: pyupgrade
-        args: [--py37-plus]
+        args: [--py38-plus]
         types: [text]
         types_or: [python, pyi]
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.991
+    rev: v1.1.1
     hooks:
     -   id: mypy
         additional_dependencies: [types-toml]
@@ -72,7 +66,7 @@ repos:
         types_or: [python, pyi]
         exclude: ^(devtools/|docs/|setup.py)
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.2
+    rev: v2.2.4
     hooks:
     -   id: codespell
         exclude: (\.ipynb$|^\.github/workflows/issue_to_jira.yml$)
@@ -95,7 +89,7 @@ repos:
     -   id: mixed-line-ending
     -   id: name-tests-test
 -   repo: https://github.com/rstcheck/rstcheck
-    rev: v6.1.1
+    rev: v6.1.2
     hooks:
     -   id: rstcheck
         additional_dependencies: [sphinx]

param_sweeps/__init__.py

@@ -6,4 +6,4 @@
 #  (see LICENSE file at the root of this source code package).
 
 
-__version__ = "0.1.4"
+__version__ = "0.1.5"

param_sweeps/driver.py

@@ -16,6 +16,7 @@
 import uuid
 from dataclasses import dataclass
 from inspect import signature
+from typing import Any
 
 import numpy as np
 from geoh5py.data import Data
@@ -140,9 +141,7 @@ def write_files(self, lookup):
 
         ifile = InputFile.read_ui_json(self.params.worker_uijson)
         with ifile.data["geoh5"].open(mode="r") as workspace:
-
             for name, trial in lookup.items():
-
                 if trial["status"] != "pending":
                     continue
 
@@ -193,11 +192,14 @@ def call_worker(ifile: InputFile):
 
     run_cmd = ifile.data["run_command"]
     module = importlib.import_module(run_cmd)
-    filt = (
-        lambda member: inspect.isclass(member)
-        and member.__module__ == run_cmd
-        and hasattr(member, "run")
-    )
+
+    def filt(member: Any) -> bool:
+        return (
+            inspect.isclass(member)
+            and member.__module__ == run_cmd
+            and hasattr(member, "run")
+        )
+
     driver = inspect.getmembers(module, filt)[0][1]
     driver.start(ifile.path_name)
 
@@ -226,7 +228,6 @@ def main(file_path):
 
 
 if __name__ == "__main__":
-
     parser = argparse.ArgumentParser(
         description="Run parameter sweep of worker driver."
     )

param_sweeps/generate.py

@@ -40,7 +40,6 @@ def generate(
         sweepfile.data.update(**update_values)
 
     for param, value in ifile.data.items():
-
         if parameters is not None and param not in parameters:
             continue
 

param_sweeps/sample_driver.py

@@ -14,7 +14,6 @@
 
 @dataclass
 class SampleParams:
-
     data_object: str | None = None
     data: str | None = None
     param: int = 1