From 80924d0d48cded4297383a106269d5c6567597db Mon Sep 17 00:00:00 2001
From: Ludger Paehler <paehlerludger@gmail.com>
Date: Sat, 10 Oct 2026 21:18:04 -0700
Subject: [PATCH 1/2] Stop tracking compiled Python files and forbid committing
 them

Nine .pyc files under koopmanrl/environments/__pycache__/ and
koopmanrl/koopman_tensor/__pycache__/ were tracked, among them the
bytecode of the removed cartpole environments. They showed up as
modified after every run and shipped stale bytecode to every clone.
They are build artefacts that Python regenerates on import, so they are
removed from the repository.

.gitignore listed __pycache__/ per directory and missed
koopmanrl/koopman_tensor/ and its observables/ package, which is how
those files got in. The per-directory entries are replaced by a general
rule, __pycache__/ and *.py[cod], that covers every directory.

Ignoring does not stop a force-add, so a local pre-commit hook,
forbid-compiled-python, fails on any .pyc, .pyo, .pyd or file under a
__pycache__/ directory. CI runs `pre-commit run --all-files` on the
tracked files, so a compiled file that is committed anyway fails the
Lint workflow.

The guides describe the new state: koopmanrl/environments/AGENTS.md no
longer warns about tracked .pyc files, and the root AGENTS.md and the
contributing page of the docs list the new hook and the ignored
compiled files.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 .gitignore                                       |  10 +++-------
 .pre-commit-config.yaml                          |   8 ++++++++
 AGENTS.md                                        |   4 ++--
 docs/docs/developers/contributing.md             |   1 +
 koopmanrl/environments/AGENTS.md                 |   2 +-
 .../__pycache__/__init__.cpython-310.pyc         | Bin 500 -> 0 bytes
 .../cartpole_control_env.cpython-310.pyc         | Bin 7565 -> 0 bytes
 .../continuous_cartpole.cpython-310.pyc          | Bin 5719 -> 0 bytes
 .../__pycache__/double_well.cpython-310.pyc      | Bin 4898 -> 0 bytes
 .../__pycache__/fluid_flow.cpython-310.pyc       | Bin 4736 -> 0 bytes
 .../__pycache__/linear_system.cpython-310.pyc    | Bin 3693 -> 0 bytes
 .../__pycache__/lorenz.cpython-310.pyc           | Bin 4639 -> 0 bytes
 .../__pycache__/__init__.cpython-310.pyc         | Bin 233 -> 0 bytes
 .../__pycache__/utils.cpython-310.pyc            | Bin 977 -> 0 bytes
 14 files changed, 15 insertions(+), 10 deletions(-)
 delete mode 100644 koopmanrl/environments/__pycache__/__init__.cpython-310.pyc
 delete mode 100644 koopmanrl/environments/__pycache__/cartpole_control_env.cpython-310.pyc
 delete mode 100644 koopmanrl/environments/__pycache__/continuous_cartpole.cpython-310.pyc
 delete mode 100644 koopmanrl/environments/__pycache__/double_well.cpython-310.pyc
 delete mode 100644 koopmanrl/environments/__pycache__/fluid_flow.cpython-310.pyc
 delete mode 100644 koopmanrl/environments/__pycache__/linear_system.cpython-310.pyc
 delete mode 100644 koopmanrl/environments/__pycache__/lorenz.cpython-310.pyc
 delete mode 100644 koopmanrl/koopman_tensor/__pycache__/__init__.cpython-310.pyc
 delete mode 100644 koopmanrl/koopman_tensor/__pycache__/utils.cpython-310.pyc

diff --git a/.gitignore b/.gitignore
index 2bbe367..f086144 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,8 +1,6 @@
-# Ignore PyCaches
-koopmanrl/__pycache__/
-koopmanrl/environments/__pycache__/
-tests/__pycache__/
-koopmanrl_utils/movies/__pycache__/
+# Ignore PyCaches and compiled Python files, in every directory
+__pycache__/
+*.py[cod]
 
 # Ignore simulation results
 runs/
@@ -18,7 +16,6 @@ tsne_koopman_tensor_results/
 skvi_policy_checks_results/
 skvi_sensitivity_checks_results/
 koopman_prediction_validation_results/
-koopmanrl_utils/__pycache__/
 
 # Output of koopmanrl_utils/koopman_regressor_comparison.py
 koopman_regressor_comparison_results/
@@ -32,4 +29,3 @@ ablation_results/
 # Output and bookkeeping of the Snakemake workflows in workflow/
 results/
 .snakemake/
-workflow/__pycache__/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ac0247a..07fcdb9 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -28,3 +28,11 @@ repos:
           - id: isort
             name: isort (python)
             args: ["--profile", "black"]
+
+    - repo: local
+      hooks:
+          - id: forbid-compiled-python
+            name: Forbid compiled Python files
+            entry: Compiled Python files (.pyc, .pyo, .pyd, __pycache__/) must not be committed
+            language: fail
+            files: '(\.py[cod]$|(^|/)__pycache__/)'
diff --git a/AGENTS.md b/AGENTS.md
index 586b80d..0e35e2e 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -32,7 +32,7 @@ workflow/                Snakemake workflows: Snakefile, rules/*.smk, helpers.py
 
 ## Running Code
 - Run everything from the repository root as a module: `uv run -m koopmanrl.<module>` or `uv run -m koopmanrl_utils.<module>`. Every algorithm and most scripts take `--help` (typed `tap` parsers).
-- Runs write TensorBoard logs to `runs/` and checkpoints to `saved_models/` in the working directory. These and the result directories of the scripts (`*_results/`, `results/`, `figures/`, `video_frames/`, `.snakemake/`) are gitignored; do not commit outputs.
+- Runs write TensorBoard logs to `runs/` and checkpoints to `saved_models/` in the working directory. These and the result directories of the scripts (`*_results/`, `results/`, `figures/`, `video_frames/`, `.snakemake/`) are gitignored; do not commit outputs. Compiled Python files (`__pycache__/`, `*.py[cod]`) are gitignored in every directory and are not tracked.
 - Do not execute `koopmanrl_utils/run_skvi_optimization.py` or `run_sakc_optimization.py` to inspect them: they take no arguments, so even `--help` starts four full Ray Tune studies. Read the source instead. Before executing any other script, check that it has an argument parser.
 - `koopmanrl.{skvi,sakc}_optuna_opt` default to `--cpu_cores_per_trial 28`, which Ray cannot schedule on a smaller machine (the study then idles forever), and to a `--storage_dir` on the authors' machine. Pass both when running them.
 - The reproduction launchers (`run_optimized_experiments`, `run_ablations`) start hundreds of 50,000-step runs by default. Use `--dry_run` to list the commands, and the filters described in their guides to run a part.
@@ -49,7 +49,7 @@ workflow/                Snakemake workflows: Snakefile, rules/*.smk, helpers.py
 
 ## Testing, Linting and CI
 - Run the tests of what you touch: `uv run pytest tests/test_<area>.py [-k <name>]`. There are no pytest markers; `uv run pytest` runs the whole suite (several minutes). Details and known failures are in `tests/AGENTS.md`.
-- `uv run pre-commit run --files <changed files>` (or `--all-files`): ruff (`--fix`, format; line length 120), isort (`--profile black`), vulture on `koopmanrl/`, and the basic pre-commit-hooks (whitespace, end of file, YAML, files > 1 MB, merge conflicts, debug statements).
+- `uv run pre-commit run --files <changed files>` (or `--all-files`): ruff (`--fix`, format; line length 120), isort (`--profile black`), vulture on `koopmanrl/`, the basic pre-commit-hooks (whitespace, end of file, YAML, files > 1 MB, merge conflicts, debug statements), and the local `forbid-compiled-python` hook, which fails on any `.pyc`/`.pyo`/`.pyd` or `__pycache__/` file.
 - CI runs only pre-commit (`lint.yml`) and the docs build (`test-deploy-docs.yml` on PRs, `deploy-docs.yml` on `main`, Node 20). It does not run pytest, so run the relevant tests locally.
 - Docs site: `cd docs && npm ci && npm run build`; the build fails on broken links.
 
diff --git a/docs/docs/developers/contributing.md b/docs/docs/developers/contributing.md
index 8ba4de0..9fe19d5 100644
--- a/docs/docs/developers/contributing.md
+++ b/docs/docs/developers/contributing.md
@@ -43,6 +43,7 @@ The repository enforces formatting and linting via pre-commit:
 - **Ruff** — linting with `--fix` (`ruff`) and formatting (`ruff-format`), line length 120
 - **isort** — import sorting with `--profile black`
 - **Vulture** — dead-code detection on `koopmanrl/` with `--min-confidence 80`
+- **forbid-compiled-python** — a local hook that fails on any compiled Python file (`.pyc`, `.pyo`, `.pyd`, `__pycache__/`); these are gitignored and must not be committed
 
 In CI, `.github/workflows/lint.yml` runs `pre-commit run --all-files` on every pull request and push to `main`, and `.github/workflows/test-deploy-docs.yml` builds this documentation site on pull requests to `main`.
 
diff --git a/koopmanrl/environments/AGENTS.md b/koopmanrl/environments/AGENTS.md
index 7916c8e..a11c152 100644
--- a/koopmanrl/environments/AGENTS.md
+++ b/koopmanrl/environments/AGENTS.md
@@ -28,6 +28,6 @@ Each environment module calls `gym.envs.registration.register` at import, under
 
 * `gym==0.23.1` is pinned; its warning that Gym is unmaintained is expected.
 * `koopmanrl_utils/movies/` plots only FluidFlow, Lorenz and DoubleWell.
-* `__pycache__/` of this directory holds tracked `.pyc` files (including those of removed cartpole environments); they show up as modified after any run. Do not commit them.
+* `__pycache__/` of this directory is regenerated on import and gitignored, like every compiled Python file of the repository; the `forbid-compiled-python` pre-commit hook rejects one that is committed anyway (e.g. force-added).
 
 See the root `AGENTS.md` for setup, testing and the working checklist.
diff --git a/koopmanrl/environments/__pycache__/__init__.cpython-310.pyc b/koopmanrl/environments/__pycache__/__init__.cpython-310.pyc
deleted file mode 100644
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From abac0f9e4fc97a76e459633401139e7f16f13530 Mon Sep 17 00:00:00 2001
From: Ludger Paehler <paehlerludger@gmail.com>
Date: Sat, 10 Oct 2026 21:24:48 -0700
Subject: [PATCH 2/2] Move the note on compiled files to the pre-commit bullet
 of AGENTS.md

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 AGENTS.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/AGENTS.md b/AGENTS.md
index 0e35e2e..5d0d6ab 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -32,7 +32,7 @@ workflow/                Snakemake workflows: Snakefile, rules/*.smk, helpers.py
 
 ## Running Code
 - Run everything from the repository root as a module: `uv run -m koopmanrl.<module>` or `uv run -m koopmanrl_utils.<module>`. Every algorithm and most scripts take `--help` (typed `tap` parsers).
-- Runs write TensorBoard logs to `runs/` and checkpoints to `saved_models/` in the working directory. These and the result directories of the scripts (`*_results/`, `results/`, `figures/`, `video_frames/`, `.snakemake/`) are gitignored; do not commit outputs. Compiled Python files (`__pycache__/`, `*.py[cod]`) are gitignored in every directory and are not tracked.
+- Runs write TensorBoard logs to `runs/` and checkpoints to `saved_models/` in the working directory. These and the result directories of the scripts (`*_results/`, `results/`, `figures/`, `video_frames/`, `.snakemake/`) are gitignored; do not commit outputs.
 - Do not execute `koopmanrl_utils/run_skvi_optimization.py` or `run_sakc_optimization.py` to inspect them: they take no arguments, so even `--help` starts four full Ray Tune studies. Read the source instead. Before executing any other script, check that it has an argument parser.
 - `koopmanrl.{skvi,sakc}_optuna_opt` default to `--cpu_cores_per_trial 28`, which Ray cannot schedule on a smaller machine (the study then idles forever), and to a `--storage_dir` on the authors' machine. Pass both when running them.
 - The reproduction launchers (`run_optimized_experiments`, `run_ablations`) start hundreds of 50,000-step runs by default. Use `--dry_run` to list the commands, and the filters described in their guides to run a part.
@@ -49,7 +49,7 @@ workflow/                Snakemake workflows: Snakefile, rules/*.smk, helpers.py
 
 ## Testing, Linting and CI
 - Run the tests of what you touch: `uv run pytest tests/test_<area>.py [-k <name>]`. There are no pytest markers; `uv run pytest` runs the whole suite (several minutes). Details and known failures are in `tests/AGENTS.md`.
-- `uv run pre-commit run --files <changed files>` (or `--all-files`): ruff (`--fix`, format; line length 120), isort (`--profile black`), vulture on `koopmanrl/`, the basic pre-commit-hooks (whitespace, end of file, YAML, files > 1 MB, merge conflicts, debug statements), and the local `forbid-compiled-python` hook, which fails on any `.pyc`/`.pyo`/`.pyd` or `__pycache__/` file.
+- `uv run pre-commit run --files <changed files>` (or `--all-files`): ruff (`--fix`, format; line length 120), isort (`--profile black`), vulture on `koopmanrl/`, the basic pre-commit-hooks (whitespace, end of file, YAML, files > 1 MB, merge conflicts, debug statements), and the local `forbid-compiled-python` hook, which fails on any `.pyc`/`.pyo`/`.pyd` or `__pycache__/` file. Compiled Python files are also gitignored in every directory, so none are tracked.
 - CI runs only pre-commit (`lint.yml`) and the docs build (`test-deploy-docs.yml` on PRs, `deploy-docs.yml` on `main`, Node 20). It does not run pytest, so run the relevant tests locally.
 - Docs site: `cd docs && npm ci && npm run build`; the build fails on broken links.