fix: release-preflight

.github/workflows/release-preflight.yml

@@ -55,15 +55,21 @@ jobs:
             exit 1
           fi
 
-      - name: Configure authenticated Git remote
+      - name: Configure Git credentials
         env:
           RELEASE_TOKEN: ${{ secrets.SEMANTIC_RELEASE_TOKEN }}
         run: |
-          git remote set-url origin https://x-access-token:${RELEASE_TOKEN}@github.com/${{ github.repository }}.git
+          set -euo pipefail
+          # Disable any credential helpers the runner may have configured
+          # (gh CLI, credential-manager, etc.) that can intercept push auth.
+          git config --local --unset-all credential.helper || true
+          git config --local credential.helper ''
+          # Use the extraheader method — the same mechanism actions/checkout
+          # uses internally. Works reliably for both fetch and push.
+          BASIC=$(echo -n "x-access-token:${RELEASE_TOKEN}" | base64)
+          git config --local http.https://github.com/.extraheader "AUTHORIZATION: basic ${BASIC}"
 
       - name: Preflight token and push checks
-        env:
-          RELEASE_TOKEN: ${{ secrets.SEMANTIC_RELEASE_TOKEN }}
         run: |
           set -euo pipefail
 
@@ -73,9 +79,9 @@ jobs:
           echo "Checking write access via dry-run push to unprotected ref..."
           test_ref="refs/preflight/sr-${GITHUB_RUN_ID}-${GITHUB_RUN_ATTEMPT}"
           if ! git push --dry-run origin "HEAD:${test_ref}" 2>&1; then
-            echo "::error::SEMANTIC_RELEASE_TOKEN exists but cannot push to ${GITHUB_REPOSITORY}."
+            echo "::error::SEMANTIC_RELEASE_TOKEN cannot push to ${GITHUB_REPOSITORY}."
             echo "::error::Ensure the PAT has Contents: Read and write (fine-grained) or 'repo' scope (classic)."
-            echo "::error::For org repos, also verify the fine-grained PAT was approved in org settings."
+            echo "::error::For org repos, verify the fine-grained PAT was approved in org settings."
             exit 1
           fi
 

.github/workflows/release.yml

@@ -103,11 +103,15 @@ jobs:
             @semantic-release/exec@6 \
             conventional-changelog-conventionalcommits@7
 
-      - name: Configure authenticated Git remote
+      - name: Configure Git credentials
         env:
           RELEASE_TOKEN: ${{ secrets.SEMANTIC_RELEASE_TOKEN || github.token }}
         run: |
-          git remote set-url origin https://x-access-token:${RELEASE_TOKEN}@github.com/${{ github.repository }}.git
+          set -euo pipefail
+          git config --local --unset-all credential.helper || true
+          git config --local credential.helper ''
+          BASIC=$(echo -n "x-access-token:${RELEASE_TOKEN}" | base64)
+          git config --local http.https://github.com/.extraheader "AUTHORIZATION: basic ${BASIC}"
 
       - name: Semantic Release
         env:

docs/spotoptim_class.qmd

@@ -0,0 +1,137 @@
+---
+title: "SpotOptim Class"
+description: "Structure of the Methods"
+---
+
+
+## Overview
+
+# TASK_VARS:
+
+* detect_var_type
+* modify_bounds_based_on_var_type
+* repair_non_numeric
+* handle_default_var_trans
+* process_factor_bounds
+
+
+# TASK_SAVE_LOAD:
+
+* get_pickle_safe_optimizer
+* reinitialize_components
+
+# TASK_DIM:
+
+* setup_dimension_reduction()
+* to_red_dim()
+* to_all_dim()
+
+# TASK_TRANSFORM:
+
+* transform_value()
+* inverse_transform_value()
+* transform_X()
+* inverse_transform_X()
+* transform_bounds()
+* map_to_factor_values()
+
+# TASK_INIT_DESIGN:
+
+* get_initial_design()
+* generate_initial_design()
+* curate_initial_design()
+* rm_initial_design_NA_values()
+* validate_x0()
+* check_size_initial_design()
+* get_best_xy_initial_design()
+
+# TASK_Surrogate:
+
+* init_surrogate()
+* _fit_surrogate()
+*_fit_scheduler()
+
+# TASK_PREDICT:
+
+* _predict_with_uncertainty()
+* _acquisition_function()
+
+# TASK_OPTIM:
+
+* evaluate_function()
+* _optimize_acquisition_tricands()
+* _prepare_de_kwargs()
+* _optimize_acquisition_de()
+* _optimize_acquisition_scipy()
+* _try_optimizer_candidates()
+* remove_nan()
+* _handle_acquisition_failure()
+* _try_fallback_strategy()
+* get_shape()
+* optimize_acquisition_func()
+* _optimize_run_task()
+* optimize()
+* execute_optimization_run()
+
+# TASK_MO:
+
+* store_mo()
+* mo2so()
+
+# TASK_OCBA:
+
+* apply_ocba()
+* get_ranks()
+* get_ocba()
+* get_ocba_X()
+
+# TASK_SELECT:
+
+* select_distant_points()
+* select_best_cluster()
+* _selection_dispatcher()
+* select_new()
+* suggest_next_infill_point()
+
+# TASK_OPTIM_SEQ:
+
+* determine_termination()
+* apply_penalty_NA()
+* update_best_main_loop()
+* handle_NA_new_points()
+* optimize_sequential_run()
+* _initialize_run()
+* update_repeats_infill_points()
+* _run_sequential_loop()
+
+# TASK_OPTIM_PARALLEL:
+
+* _update_storage_steady()
+* optimize_steady_state()
+
+# TASK_STATS:
+
+* init_storage()
+* update_storage()
+* update_stats()
+* update_success_rate()
+* get_success_rate()
+* aggregate_mean_var()
+* get_best_hyperparameters
+
+# TASK_RESULTS:
+
+* save_result()
+* load_result()
+* save_experiment()
+* load_experiment()
+* get_result_filename()
+* get_experiment_filename()
+* print_results()
+* print_best()
+* get_results_table()
+* get_design_table()
+* gen_design_table()
+* get_importance()
+* sensitivity_spearman()
+* get_stars()