Merge pull request #787 from open-energy-transition/merge-upstream-260706

Merge changes from upstream

Author: tgilon

.github/ISSUE_TEMPLATE/1-bug-community.yaml

@@ -11,6 +11,8 @@ body:
 
       Please do not post usage questions here. Ask them on the [PyPSA/Open-TYNDP Discord channel](https://discord.com/channels/911692131440148490/1414977512089321564) or contact tyndp@openenergytransition.org.
 
+      Please write this issue description yourself. Any potentially verbose AI-generated content should be marked.
+
 - type: checkboxes
   id: version_checks
   attributes:

.github/ISSUE_TEMPLATE/2-feature-community.yaml

@@ -11,6 +11,8 @@ body:
 
       Please do not post usage questions here. Ask them on the [PyPSA/Open-TYNDP Discord channel](https://discord.com/channels/911692131440148490/1414977512089321564) or contact tyndp@openenergytransition.org.
 
+      Please write this issue description yourself. Any potentially verbose AI-generated content should be marked.
+
 - type: checkboxes
   id: affected_component
   attributes:

.github/ISSUE_TEMPLATE/3-bug-maintainer.yaml

@@ -11,6 +11,8 @@ body:
 
       Please do not post usage questions here. Ask them on the [PyPSA/Open-TYNDP Discord channel](https://discord.com/channels/911692131440148490/1414977512089321564) or contact tyndp@openenergytransition.org.
 
+      Please write this issue description yourself. Any potentially verbose AI-generated content should be marked.
+
 - type: checkboxes
   id: version_checks
   attributes:

.github/ISSUE_TEMPLATE/4-feature-maintainer-parent.yaml

@@ -12,6 +12,8 @@ body:
 
       This template is for high-level parent issues that will be broken down into sub-issues. Use the ["Feature - Sub Issue (Maintainer)"](https://github.com/open-energy-transition/open-tyndp/issues/new?template=5-feature-maintainer-sub.yaml) template for detailed feature requests. Security and risk assessment is captured at this sub-issue level.
 
+      Please write this issue description yourself. Any potentially verbose AI-generated content should be marked.
+
 - type: checkboxes
   id: affected_component
   attributes:

.github/ISSUE_TEMPLATE/5-feature-maintainer-sub.yaml

@@ -12,6 +12,8 @@ body:
 
       This template is for detailed feature requests. Use the ["Feature - Parent Issue (Maintainer)"](https://github.com/open-energy-transition/open-tyndp/issues/new?template=4-feature-maintainer-parent.yaml) template for high-level parent issues that will be broken down into sub-issues.
 
+      Please write this issue description yourself. Any potentially verbose AI-generated content should be marked.
+
 - type: input
   id: parent_issue
   attributes:

.github/ISSUE_TEMPLATE/6-spike-maintainer.yaml

@@ -12,6 +12,8 @@ body:
 
       Spikes are exploratory issues meant to gather information and explore concepts. They typically don't result in PRs but help inform future implementation decisions.
 
+      Please write this issue description yourself. Any potentially verbose AI-generated content should be marked.
+
 - type: input
   id: parent_issue
   attributes:

.github/pull_request_template.md

@@ -22,6 +22,7 @@ Closes # (if applicable).
 - [ ] Changes are tested locally and behave as expected.
 - [ ] Code and workflow changes are documented.
 - [ ] A release note entry is added to `doc/release_notes.md`.
+- [ ] The description is human-written and any AI-generated content is marked.
 
 **If applicable:**
 - [ ] Changes in configuration options are reflected in `scripts/lib/validation`.

.github/workflows/security-scan.yaml

@@ -45,12 +45,15 @@ jobs:
         add-cpes-if-none: true
         output-format: sarif
 
-    # Point alerts to pixi.lock so githubs path scoped PR check registers it
-    - name: Rewrite SARIF locations to pixi.lock
+    # Set uri=pixi.lock for a readable location, and fingerprint each alert by
+    # CVE id so code scanning matches against the master baseline by CVE, not line.
+    - name: Normalize SARIF (pixi.lock location + CVE fingerprint)
       run: |
-        jq '.runs[].results[].locations[].physicalLocation.artifactLocation.uri = "pixi.lock"' \
-          "${{ steps.scan.outputs.sarif }}" > rewritten.sarif
-        mv rewritten.sarif "${{ steps.scan.outputs.sarif }}"
+        jq '.runs[].results[] |= (
+              .locations[].physicalLocation.artifactLocation.uri = "pixi.lock"
+              | .partialFingerprints = {"grypeCve/v1": .ruleId}
+            )' "${{ steps.scan.outputs.sarif }}" > normalized.sarif
+        mv normalized.sarif "${{ steps.scan.outputs.sarif }}"
 
     - name: Upload SARIF
       if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository

Snakefile

@@ -60,16 +60,19 @@ for scenario_name, scenario_overrides in scenarios.items():
         ) from e
 
 RDIR = get_rdir(run)
+PROJ_DIR = Path(workflow.snakefile).parent
+
 shadow_config = get_shadow(run)
 
 shared_resources = run["shared_resources"]["policy"]
 exclude_from_shared = run["shared_resources"]["exclude"]
 logs = path_provider("logs/", RDIR, shared_resources, exclude_from_shared)
 benchmarks = path_provider("benchmarks/", RDIR, shared_resources, exclude_from_shared)
 resources = path_provider("resources/", RDIR, shared_resources, exclude_from_shared)
-scripts = script_path_provider(Path(workflow.snakefile).parent)
+scripts = script_path_provider(PROJ_DIR)
 
 RESULTS = "results/" + RDIR
+workflow.default_target = config["run"]["default_target_rule"]
 
 
 localrules:
@@ -207,7 +210,6 @@ def input_all_tyndp(w):
 
 
 rule all:
-    default_target: True
     input:
         input_all_tyndp,
         expand(RESULTS + "graphs/costs.pdf", run=config["run"]["name"]),
@@ -396,6 +398,8 @@ rule rulegraph:
         pdf=resources("dag_rulegraph.pdf"),
         png=resources("dag_rulegraph.png"),
         svg=resources("dag_rulegraph.svg"),
+    params:
+        default_target=workflow.default_target,  # track default target to ensure rule is re-triggered
     message:
         "Creating RULEGRAPH dag in multiple formats using the final configuration."
     shell:
@@ -433,6 +437,8 @@ rule filegraph:
         pdf=resources("dag_filegraph.pdf"),
         png=resources("dag_filegraph.png"),
         svg=resources("dag_filegraph.svg"),
+    params:
+        default_target=workflow.default_target,  # track default target to ensure rule is re-triggered
     message:
         "Creating FILEGRAPH dag in multiple formats using the final configuration."
     shell:

config/config.default.yaml

@@ -33,6 +33,7 @@ run:
     policy: false
     exclude: []
   use_shadow_directory: false
+  default_target_rule: all
 
 # docs in https://open-tyndp.readthedocs.io/en/latest/configuration.html#foresight
 foresight: overnight
@@ -1311,6 +1312,13 @@ solving:
       primal_feasibility_tolerance: 1.0e-05
       dual_feasibility_tolerance: 1.0e-05
       random_seed: 123
+    "highs-hipo":
+      solver: hipo
+      parallel: 'on'
+      primal_feasibility_tolerance: 1.0e-05
+      dual_feasibility_tolerance: 1.0e-05
+      random_seed: 123
+      run_crossover: 'off'
     "gurobi-default":
       threads: 32
       method: 2
@@ -1394,6 +1402,8 @@ solving:
 
 # docs in https://open-tyndp.readthedocs.io/en/latest/configuration.html#data
 data:
+  version_files:
+  - data/versions.csv
   hotmaps_industrial_sites:
     source: archive
     version: latest