Merge main into GH-279/initial-python-linting

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,70 @@
+name: Bug Report
+description: File a bug report
+title: "[Bug]: "
+
+body:
+  - type: dropdown
+    id: label
+    attributes:
+      label: Label
+      description: Which label(s) describe this issue?
+      multiple: true
+      options:
+        - bug
+        - batch
+        - config.writer
+        - documentation
+        - enhancement
+        - gempyor
+        - good first issue
+        - help wanted
+        - inference
+        - invalid
+        - meta/workflow
+        - operations
+        - performance
+        - post-processing
+        - question
+        - quick issue
+        - revisit ASAP
+        - seeding
+        - submission
+        - wontfix
+    validations:
+      required: true
+
+  - type: dropdown
+    id: priority
+    attributes:
+      label: Priority Label
+      description: What priority level is this issue?
+      options:
+        - low priority
+        - medium priority
+        - high priority
+    validations:
+      required: true
+
+  - type: textarea
+    id: what-happened
+    attributes:
+      label: Describe the bug/issue
+      placeholder: A clear and concise description of what the issue is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: to-reproduce
+    attributes:
+      label: To Reproduce
+      placeholder: Run code '...' and expect this error '...'
+    validations:
+      required: false
+
+  - type: input
+    id: environment
+    attributes:
+      label: Environment, if relevant
+      placeholder: OS (e.g. Ubuntu 22.04, macOS 14.5, etc.). R and/or Python version (terminal command `R --version` or `python --version`). fleiMoP branch and/or commit if relevant (`git rev-parse HEAD`)
+    validations:
+      required: false

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,70 @@
+name: Feature Request
+description: File a feature request
+title: "[Feature request]: "
+
+body:
+  - type: dropdown
+    id: label
+    attributes:
+      label: Label
+      description: Which label(s) describe this issue?
+      multiple: true
+      options:
+        - bug
+        - batch
+        - config.writer
+        - documentation
+        - enhancement
+        - gempyor
+        - good first issue
+        - help wanted
+        - inference
+        - invalid
+        - meta/workflow
+        - operations
+        - performance
+        - post-processing
+        - question
+        - quick issue
+        - revisit ASAP
+        - seeding
+        - submission
+        - wontfix
+    validations:
+      required: true
+
+  - type: dropdown
+    id: priority
+    attributes:
+      label: Priority Label
+      description: What priority level is this issue?
+      options:
+        - low priority
+        - medium priority
+        - high priority
+    validations:
+      required: true
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Is your feature request related to a problem? Please describe.
+      placeholder: A clear and concise description of what the problem is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: relevant-relationship
+    attributes:
+      label: Is your feature request related to a new application, scenario round, pathogen? Please describe.
+      placeholder: A clear and concise description of th application, round, etc. that the feature addresses. 
+    validations:
+      required: false
+
+  - type: textarea
+    id: solution
+    attributes:
+      label: Describe the solution you'd like
+      placeholder: A clear and concise description of what you want to happen. 
+    validations:
+      required: true

.github/labeler.yml

@@ -0,0 +1,46 @@
+batch:
+  - '(batch)'
+bug:
+  - '(bug)'
+config.writer:
+  - '(config.writer)'
+documentation:
+  - '(documentation)'
+enhancement:
+  - '(enhancement)'
+gempyor:
+  - '(gempyor)'
+good first issue:
+  - '(good first issue)'
+help wanted:
+  - '(help wanted)'
+high priority:
+  - '(high priority)'
+inference:
+  - '(inference)'
+invalid:
+  - '(invalid)'
+low priority:
+  - '(low priority)'
+medium priority:
+  - '(medium priority)'
+meta/workflow:
+  - '(meta|workflow)'
+operations:
+  - '(operations)'
+performance:
+  - '(performance)'
+post-processing:
+  - '(post-processing)'
+question:
+  - '(question)'
+quick issue:
+  - '(quick issue)'
+revisit ASAP:
+  - '(revisit ASAP)'
+seeding:
+  - '(seeding)'
+submission:
+  - '(submission)' 
+wontfix:
+  - '(wontfix)'

.github/pull_request_template.yml

@@ -0,0 +1,24 @@
+name: Pull Request
+description: Pull request template
+
+body:
+  - type: textarea
+    id: describe-changes
+    attributes:
+      label: Describe your changes.
+    validations:
+      required: true
+
+  - type: textarea
+    id: what-it-addresses
+    attributes:
+      label: What does your pull request address? Tag relevant issues.
+    validations:
+      required: true
+
+  - type: textarea
+    id: relevant-team-members
+    attributes:
+      label: Tag relevant team members.
+    validations:
+      required: false 

.github/workflows/labeler.yml

@@ -0,0 +1,18 @@
+name: "Issue Labeler"
+on:
+  issues:
+    types: [opened, edited]
+
+permissions:
+  issues: write
+  contents: read
+
+jobs:
+  triage:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: github/issue-labeler@v3.3 
+      with:
+        configuration-path: .github/labeler.yml
+        enable-versioned-regex: 0
+        repo-token: ${{ github.token }}

flepimop/gempyor_pkg/tests/file_paths/test_run_id.py

@@ -1,4 +1,4 @@
-from datetime import datetime, timezone
+from datetime import datetime, timedelta, timezone
 import re
 
 import pytest
@@ -23,7 +23,7 @@ def test_get_run_id_default_timestamp(self) -> None:
 
         # Run id is between before/after
         before = before.replace(microsecond=0)
-        after = after.replace(microsecond=0, second=after.second + 1)
+        after = (after + timedelta(seconds=1)).replace(microsecond=0)
         run_time = datetime.strptime(rid, "%Y%m%d_%H%M%S")
         assert run_time >= before
         assert run_time <= after