Remove obsolete notebooks

.github/scripts/generate_conda_locks.sh

@@ -5,7 +5,7 @@ readonly SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 readonly REPO_ROOT="$(cd "${SCRIPT_DIR}/../.." && pwd)"
 readonly LOCK_DIR="${REPO_ROOT}/.github/conda-lock"
 readonly TEMP_ENV_FILE="${REPO_ROOT}/env_tmp.yml"
-readonly PINNED_CONDA_LOCK_VERSION="4.0.0"
+readonly PINNED_CONDA_LOCK_VERSION="4.0.2"
 readonly PYTHON_VERSIONS=("3.12" "3.13" "3.14")
 
 require_command() {

.github/workflows/ci-reusable.yml

@@ -8,7 +8,7 @@
 #
 # STAGE 1: QUICK VALIDATION (Parallel with Stage 2)
 # - Goal: 2-3 minute feedback on common PR issues.
-# - Actions: Linting, formatting, and Jupyter Notebook cleanliness checks.
+# - Actions: Linting and formatting.
 # - Optimization: Uses a dedicated conda cache (key suffix "-lint") that is
 #   intentionally separate from the full-matrix cache.  The two jobs run in
 #   parallel and would otherwise race to write the same cache key; because
@@ -60,7 +60,7 @@ on:
 env:
   CONDA_ENV: firecrown_developer
   CACHE_VERSION: 34
-  CONDA_LOCK_VERSION: "4.0.0"
+  CONDA_LOCK_VERSION: "4.0.2"
 
 jobs:
   quick-validation:
@@ -171,9 +171,6 @@ jobs:
           echo "starting make lint"
           make lint
           echo "done with make lint"
-      - name: Ensure clear Jupyter Notebooks
-        uses: ResearchSoftwareActions/EnsureCleanNotebooksAction@1.1
-
   firecrown-miniforge:
     name: (${{ matrix.os }}, py${{ matrix.python-version }})${{ matrix.coverage && ' + coverage' || '' }}
     runs-on: ${{ matrix.os }}-latest

.gitignore

@@ -3,7 +3,6 @@ dist/
 build/
 __pycache__/
 examples/output_*
-examples/*/.ipynb_checkpoints/*
 examples/srd_sn/sndata/
 .idea
 .project
@@ -23,8 +22,6 @@ examples/output_*
 examples/desc_srd_v1/srd_data/LSST_DESC_SRD_v1_release
 
 *.pytest_cache
-*.ipynb_checkpoints
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -102,9 +99,6 @@ docs/api
 # PyBuilder
 target/
 
-# Jupyter Notebook
-.ipynb_checkpoints
-
 # IPython
 profile_default/
 ipython_config.py

CONTRIBUTING.md

@@ -86,7 +86,7 @@ To regenerate lockfiles and manage the lockfile generation process, see
 Developers must have `conda-lock` installed to regenerate lockfiles. Install it with:
 
 ```bash
-pip install conda-lock==4.0.0
+pip install conda-lock==4.0.2
 ```
 
 The `CONTRIBUTING_ADVANCED.md` file contains detailed information about lockfile management and the CI system.

CONTRIBUTING_ADVANCED.md

@@ -177,15 +177,15 @@ come from the branch named in `ref`.
 
 Firecrown uses `conda-lock` to generate reproducible lockfiles stored in `.github/conda-lock/`. The lockfiles use the unified multi-platform format (`py{version}.conda-lock.yml`) which bundles all supported Python versions (3.12-3.14) and platforms (linux-64, osx-arm64) in a single file per Python version.
 
-**Generating lockfiles**: Run `make conda-lock` to regenerate all lockfiles. This requires `conda-lock==4.0.0` installed in your development environment:
+**Generating lockfiles**: Run `make conda-lock` to regenerate all lockfiles. This requires `conda-lock==4.0.2` installed in your development environment:
 
 ```bash
-pip install conda-lock==4.0.0
+pip install conda-lock==4.0.2
 ```
 
 **Verifying lockfiles**: Before pushing, run `make conda-lock-check` to confirm the lockfiles match the current `environment.yml` and git HEAD.
 
-**CI behavior**: CI jobs install `conda-lock` via `python -m pip install conda-lock==4.0.0` and use `conda-lock install` to create environments from the lockfiles. This ensures pip dependencies (`cobaya`, `isitgr`, `lsstdesc-crow`, `pygobject-stubs`) are resolved and installed as part of the locked environment, not as a separate step.
+**CI behavior**: CI jobs install `conda-lock` via `python -m pip install conda-lock==4.0.2` and use `conda-lock install` to create environments from the lockfiles. This ensures pip dependencies (`cobaya`, `isitgr`, `lsstdesc-crow`, `pygobject-stubs`) are resolved and installed as part of the locked environment, not as a separate step.
 
 **Cache keys**: CI uses lockfile hashes in cache keys (e.g., `conda-Linux-X64-py3.12-lock-{hash}-v34-lint`) to invalidate caches when dependencies change.
 

Makefile

@@ -375,7 +375,7 @@ clean-coverage:  ## Remove coverage reports
 	git clean -fdX $(CLEAN_EXCLUDES) -- coverage.json coverage.xml .coverage .coverage.* $(HTMLCOV_DIR)
 
 clean-docs:  ## Remove built documentation
-	git clean -fdX $(CLEAN_EXCLUDES) -- $(DOCS_BUILD_DIR) $(TUTORIAL_OUTPUT_DIR) $(AUTOAPI_BUILD_DIR)
+	git clean -fdX $(CLEAN_EXCLUDES) -- $(DOCS_BUILD_DIR) $(TUTORIAL_OUTPUT_DIR) $(AUTOAPI_BUILD_DIR) $(TUTORIAL_DIR)/.quarto $(TUTORIAL_DIR)/_site
 
 clean-build:  ## Remove build artifacts
 	git clean -fdX $(CLEAN_EXCLUDES) -- build/ dist/ *.egg-info/ firecrown/fctools/__pycache__ tests/__pycache__