docs: set up Sphinx + ReadTheDocs and reorganize the documentation (#13)

Reorganize docs/ into a Diátaxis-style tree (guide / reference / studies /
maintenance / archive) and add a Sphinx + MyST documentation site wired for
ReadTheDocs.

Site / toolchain:
* .readthedocs.yaml + docs/conf.py (furo, MyST-Parser, autodoc + napoleon for
  the NumPy-style docstrings, intersphinx to cobra/numpy/pandas/scipy).
* docs/requirements.txt; docs/index.md landing page + master toctree.
* Full API reference auto-generated from docstrings — one automodule page per
  subpackage, honoring each __all__.
* 7 task-oriented user-guide pages + quickstart; section index pages.
* CHANGELOG.md / IMPROVEMENTS.md are {include}-d into the site.

Link hygiene (the move + include changed relative depth):
* All intra-docs cross-links updated to the new section paths.
* Repo-file links (src/scripts/tests) and the included root files use absolute
  GitHub URLs so they resolve on both GitHub and the RTD site.
* README/CHANGELOG/IMPROVEMENTS doc links remapped to the new paths.

Quality / CI:
* Tiny docstring formatting fixes (blank line before Parameters / bullet lists,
  literal block in binaries.py) so autodoc renders cleanly. Build is
  warning-clean under `sphinx-build -W`.
* New `docs` CI job builds the site with `-W --keep-going`.

Author: edkerk

.github/workflows/ci.yml

@@ -46,3 +46,20 @@ jobs:
       # skip themselves when ``optlang.gurobi_interface`` cannot import.
       - run: pip install -e ".[dev,plotting,excel]"
       - run: pytest -q --maxfail=5 --durations=20
+
+  docs:
+    name: docs
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+          cache-dependency-path: pyproject.toml
+      - run: pip install --upgrade pip
+      # The package (with autodoc's import-time extras) plus the docs toolchain.
+      - run: pip install -e ".[excel,plotting]" -r docs/requirements.txt
+      # ``-W --keep-going`` keeps the docs build warning-clean; mirrors the
+      # ReadTheDocs build (docs/conf.py + .readthedocs.yaml).
+      - run: sphinx-build -b html -W --keep-going docs docs/_build/html

.gitignore

@@ -22,6 +22,9 @@ env/
 .DS_Store
 Thumbs.db
 
+# Docs build output
+docs/_build/
+
 # Tooling caches
 .claude/
 

.readthedocs.yaml

@@ -0,0 +1,29 @@
+# ReadTheDocs build configuration
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+
+sphinx:
+  configuration: docs/conf.py
+  # Build fails on warnings would be too strict while the API docstrings are
+  # still being filled in; keep warnings visible but non-fatal.
+  fail_on_warning: false
+
+python:
+  install:
+    # Install the package itself (with the optional extras autodoc needs to
+    # import every module) plus the docs-only toolchain.
+    - method: pip
+      path: .
+      extra_requirements:
+        - excel
+        - plotting
+    - requirements: docs/requirements.txt
+
+formats:
+  - pdf
+  - htmlzip

CHANGELOG.md

@@ -1,12 +1,12 @@
 # Changelog
 
 Milestones in the raven-python port. For function-level status see
-[docs/raven_migration.md](docs/raven_migration.md); for open work see
-[docs/todo.md](docs/todo.md).
+[docs/raven_migration.md](https://github.com/SysBioChalmers/raven-python/blob/develop/docs/reference/migration.md); for open work see
+[docs/todo.md](https://github.com/SysBioChalmers/raven-python/blob/develop/docs/reference/todo.md).
 
 ## Infrastructure
 
-* **GitHub Actions CI** ([.github/workflows/ci.yml](.github/workflows/ci.yml)) —
+* **GitHub Actions CI** ([.github/workflows/ci.yml](https://github.com/SysBioChalmers/raven-python/blob/develop/.github/workflows/ci.yml)) —
   ruff + pytest matrix over Python 3.11/3.12/3.13. Tests that require Gurobi
   auto-skip (no Gurobi on free runners); the known HiGHS upstream blocker
   (`hybrid_interface.Configuration` rejects `lp_method='primal'`) is marked
@@ -33,7 +33,7 @@ fixes with matching MATLAB back-port proposals in IMPROVEMENTS.md (FS4, B2).
   bug to `check_model`; the actual code is in `balance.py`.
 
 Two new regression tests (F3 in `test_analysis_fseof.py`, F5 in
-`test_utils_balance.py`). [docs/known_issues.md](docs/known_issues.md) now
+`test_utils_balance.py`). [docs/known_issues.md](https://github.com/SysBioChalmers/raven-python/blob/develop/docs/reference/known_issues.md) now
 fully closed (all sections A–F).
 
 ## Quality sweep — known-issues sections C / D / E
@@ -68,7 +68,7 @@ download (defensive, needs urlopen mocking).
 
 ## Quality sweep — known-issues section B
 
-Closed all four "silent misbehaviour" items from [docs/known_issues.md](docs/known_issues.md):
+Closed all four "silent misbehaviour" items from [docs/known_issues.md](https://github.com/SysBioChalmers/raven-python/blob/develop/docs/reference/known_issues.md):
 * `merge_models` warns on `formula` / `charge` conflicts when two source models
   share a name[comp] but disagree (used to silently keep the first-seen).
 * `add_reactions_from_equations` warns when creating a metabolite in an
@@ -82,7 +82,7 @@ Four new regression tests cover them.
 
 ## Quality sweep — known-issues section A
 
-Closed all six "latent edge-case bug" items from [docs/known_issues.md](docs/known_issues.md):
+Closed all six "latent edge-case bug" items from [docs/known_issues.md](https://github.com/SysBioChalmers/raven-python/blob/develop/docs/reference/known_issues.md):
 * `add_reactions_from_equations` no longer misparses `"2 oxoglutarate"` (or any
   leading-number metabolite name) — the resolver tries the full token before
   splitting off a coefficient.
@@ -101,45 +101,45 @@ Six new regression tests cover the user-reachable cases.
 
 ## Phase 7 — Localization
 
-* **Sub-cellular localisation by MILP.** [`localization.predict_localization`](src/raven_python/localization/predict.py)
-  + [`apply_localization`](src/raven_python/localization/predict.py). Deterministic (not simulated
+* **Sub-cellular localisation by MILP.** [`localization.predict_localization`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/localization/predict.py)
+  + [`apply_localization`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/localization/predict.py). Deterministic (not simulated
   annealing); caller-passed `reactions_to_relocate` set with everything else pinned;
   incomplete-model tolerant (no silent reaction removal); `apply=False` returns a diff
   preview; multi-compartment by default with primary-free, extras-penalised scoring.
-* **Predictor loaders.** [`load_wolfpsort`, `load_deeploc`](src/raven_python/localization/scores.py),
+* **Predictor loaders.** [`load_wolfpsort`, `load_deeploc`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/localization/scores.py),
   with the `gene × compartment` DataFrame contract open for any predictor.
-* **Compartment helpers** ([`manipulation/compartments.py`](src/raven_python/manipulation/compartments.py)):
+* **Compartment helpers** ([`manipulation/compartments.py`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/manipulation/compartments.py)):
   `merge_compartments`, `copy_to_compartment` — useful standalone for model curation.
-* **Real-data validation on yeast-GEM** ([docs/yeast_localization_benchmark.md](docs/yeast_localization_benchmark.md))
+* **Real-data validation on yeast-GEM** ([docs/yeast_localization_benchmark.md](https://github.com/SysBioChalmers/raven-python/blob/develop/docs/studies/yeast_localization_benchmark.md))
   — accuracy 0.72 → 0.39 on 298 GPR'd reactions as confident predictor mis-scoring rises
   from 0 % to 50 %; perfect on compartments with disjoint gene sets (c/g/lp/p/v/vm), and
   surfaces a `transport_cost` calibration insight for soft-probability score tables.
 
 ## Phase 5 — Data integration & analysis
 
-* **Reporter metabolites, FSEOF, random sampling** ([`analysis/`](src/raven_python/analysis/)).
-* **HPA omics ingestion** ([`omics.parse_hpa`, `parse_hpa_rna`, `hpa_gene_scores`, `rna_gene_scores`](src/raven_python/omics/hpa.py))
+* **Reporter metabolites, FSEOF, random sampling** ([`analysis/`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/analysis/)).
+* **HPA omics ingestion** ([`omics.parse_hpa`, `parse_hpa_rna`, `hpa_gene_scores`, `rna_gene_scores`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/omics/hpa.py))
   — pandas-tidy DataFrames replace RAVEN's sparse-matrix layout; scoring adapters reuse the
   existing GPR walk.
-* **N-model comparison** ([`comparison.compare_models`](src/raven_python/comparison/compare.py)).
+* **N-model comparison** ([`comparison.compare_models`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/comparison/compare.py)).
 * **Dynamic FBA** is **not ported** — established Python packages cover it (`dfba`,
   `reframed`, `mewpy`).
 
 ## Phase 4d — ftINIT
 
-* **ftINIT pipeline** ([`init.ftinit`](src/raven_python/init/ftinit.py)) — staged MILP, linear merge,
+* **ftINIT pipeline** ([`init.ftinit`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/init/ftinit.py)) — staged MILP, linear merge,
   task-aware gap-filling, gene pruning.
 * **Validated against MATLAB RAVEN on Human-GEM.** 5 Hart2015 cell-line models;
   Jaccard 0.973–0.977 (no-task) and 0.978–0.980 (task-constrained). See
-  [docs/humangem_validation.md](docs/humangem_validation.md).
-* **Parameter calibration & input-robustness study** ([docs/init_param_calibration.md](docs/init_param_calibration.md))
+  [docs/humangem_validation.md](https://github.com/SysBioChalmers/raven-python/blob/develop/docs/studies/humangem_validation.md).
+* **Parameter calibration & input-robustness study** ([docs/init_param_calibration.md](https://github.com/SysBioChalmers/raven-python/blob/develop/docs/studies/init_param_calibration.md))
   — `mip_gap=0.01` is the genome-scale full-pipeline sweet spot (~37% faster than 0.001 at
   Jaccard 0.995); pipeline is robust to expression noise (Jaccard 0.92–0.95) but sensitive
   to sparsity (50–70% dropout → Jaccard 0.59–0.71); the task + gap-fill layer keeps the
   essential-task pass-rate at 67–69/69 across the gradient, whereas tINIT-without-it passes
   only 35/69 even on clean data.
-* **Cross-solver portability** ([docs/init_solver_benchmark.md](docs/init_solver_benchmark.md))
-  + [`tests/test_init_solvers.py`](tests/test_init_solvers.py): Gurobi and GLPK pass at toy
+* **Cross-solver portability** ([docs/init_solver_benchmark.md](https://github.com/SysBioChalmers/raven-python/blob/develop/docs/studies/init_solver_benchmark.md))
+  + [`tests/test_init_solvers.py`](https://github.com/SysBioChalmers/raven-python/blob/develop/tests/test_init_solvers.py): Gurobi and GLPK pass at toy
   scale; only Gurobi is viable at genome scale today (HiGHS hits an upstream optlang
   `clone()` bug; GLPK ignores `configuration.timeout` on MIP).
 * **Engineering wins surfaced by the genome-scale work:** `check_tasks` and
@@ -149,25 +149,25 @@ Six new regression tests cover the user-reachable cases.
 
 ## Phase 4c — tINIT
 
-* **INIT MILP and the tINIT pipeline** ([`init.run_init`](src/raven_python/init/init.py),
-  [`init.get_init_model`](src/raven_python/init/build.py)). Clean optlang reformulation;
+* **INIT MILP and the tINIT pipeline** ([`init.run_init`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/init/init.py),
+  [`init.get_init_model`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/init/build.py)). Clean optlang reformulation;
   RNA-seq scoring via `5·ln(level/ref)`-clamped.
 
 ## Phase 4b — Gap-filling
 
-* **Connectivity gap-filling** ([`gapfilling.connect_blocked_reactions`](src/raven_python/gapfilling/fill.py))
+* **Connectivity gap-filling** ([`gapfilling.connect_blocked_reactions`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/gapfilling/fill.py))
   — MILP. Targeted (toward objective) mode delegates to `cobra.gapfill`.
 
 ## Phase 4a — Metabolic tasks
 
-* **Task list parsing + `check_tasks`** ([`tasks/`](src/raven_python/tasks/)).
+* **Task list parsing + `check_tasks`** ([`tasks/`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/tasks/)).
 
 ## Phase 3 — Reconstruction
 
 * **Homology-based draft** from a template GEM + BLAST/DIAMOND wrappers
-  ([`reconstruction/homology/`](src/raven_python/reconstruction/homology/)) — with structured
+  ([`reconstruction/homology/`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/reconstruction/homology/)) — with structured
   improvements over RAVEN's `getModelFromHomology` (see IMPROVEMENTS H1–H6).
-* **KEGG five-step pipeline** ([`reconstruction/kegg/`](src/raven_python/reconstruction/kegg/)):
+* **KEGG five-step pipeline** ([`reconstruction/kegg/`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/reconstruction/kegg/)):
   dump → parser → HMM library builder → species model → HMM-query draft.
 * **MetaCyc reconstruction** **not ported** (and flagged for removal from MATLAB RAVEN —
   see IMPROVEMENTS R-MetaCyc).
@@ -176,17 +176,17 @@ Six new regression tests cover the user-reachable cases.
 
 * **YAML** aligned to cobra's `!!omap` writer + RAVEN-only fields preserved into `.notes`,
   plus geckopy `ec-*` for enzyme-constrained models
-  ([`io/yaml.py`](src/raven_python/io/yaml.py)).
+  ([`io/yaml.py`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/io/yaml.py)).
 * **SIF**, **Excel export**, and **Standard-GEM `model/<fmt>/…` git layout**
-  ([`io/`](src/raven_python/io/)). Excel import intentionally excluded.
+  ([`io/`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/io/)). Excel import intentionally excluded.
 
 ## Phase 1 — Foundation
 
-* **GPR / balance / validation / parsing helpers** ([`utils/`](src/raven_python/utils/)) —
+* **GPR / balance / validation / parsing helpers** ([`utils/`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/utils/)) —
   cobra-absent bits only; the rest are cheatsheeted.
-* **Manipulation ergonomic layer** ([`manipulation/`](src/raven_python/manipulation/)) —
+* **Manipulation ergonomic layer** ([`manipulation/`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/manipulation/)) —
   add/change/remove/transport/transfer/merge/simplify/variance + adopted transforms.
-* **External-binary resolver** ([`binaries.py`](src/raven_python/binaries.py)) — version-pinned
+* **External-binary resolver** ([`binaries.py`](https://github.com/SysBioChalmers/raven-python/blob/develop/src/raven_python/binaries.py)) — version-pinned
   release-ZIP registry, SHA256-verified cache.
 
 ## Phase 0 — Scaffold