CRAMM 1.0.0__tar.gz

cramm-1.0.0/CRAMM.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: CRAMM
+Version: 1.0.0
+Summary: CRAMM — general-purpose hyperspectral mineral identification toolkit (USGS MICA, extended: depth-ratio rules + quantitative muscovite mapping; sensor-agnostic, EMIT L2A built in)
+Author: Shijie Li
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/leecugb/cramm
+Project-URL: Repository, https://github.com/leecugb/cramm
+Project-URL: Issues, https://github.com/leecugb/cramm/issues
+Keywords: hyperspectral,EMIT,mineral,MICA,USGS,remote-sensing
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: GIS
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: netCDF4
+Requires-Dist: pyproj
+Requires-Dist: pyresample
+Requires-Dist: threadpoolctl
+Provides-Extra: tiff
+Requires-Dist: gdal; extra == "tiff"
+Provides-Extra: pdf
+Requires-Dist: matplotlib; extra == "pdf"
+Provides-Extra: all
+Requires-Dist: gdal; extra == "all"
+Requires-Dist: matplotlib; extra == "all"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: matplotlib; extra == "test"
+Dynamic: license-file
+
+# CRAMM
+
+[![PyPI](https://img.shields.io/pypi/v/cramm)](https://pypi.org/project/cramm/)
+[![Python](https://img.shields.io/pypi/pyversions/cramm)](https://pypi.org/project/cramm/)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.22024483-blue.svg)](https://doi.org/10.5281/zenodo.22024483)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/leecugb/cramm/blob/main/LICENSE)
+![Platform](https://img.shields.io/badge/platform-Windows%20%7C%20Linux%20%7C%20macOS-lightgrey)
+
+**General-purpose hyperspectral mineral identification toolkit** — built on
+the USGS MICA (Material Identification and Characterization Algorithm)
+decision-rule system. The classification core is **sensor-agnostic**: it works
+on any VNIR–SWIR reflectance cube given its band configuration (center
+wavelengths, FWHM, valid-band mask), because the bundled splib06b reference
+spectra are resampled to the sensor's bands at runtime. EMIT L2A is simply the
+built-in data reader — one supported input type, not the defining one.
+
+CRAMM extends MICA in three ways:
+
+1. **An enhanced rule schema.** CRAMM adds an optional secondary-feature
+   depth-ratio constraint (`max_depth_ratio_feat1_over_feat0`) that rejects
+   pixels whose secondary absorption is too deep relative to the primary
+   2.2 µm feature — suppressing white-mica false positives that pass the
+   original five-layer MICA filtering. Nine bundled rules (muscovite, illite,
+   kaolinite–muscovite mixtures) carry the new constraint; any custom rule
+   can opt in. See *Enhancements over USGS MICA*.
+2. **Wavelength-arbitrated muscovite subtyping.** MICA labels a pixel
+   "muscovite_lowAl / medAl / medhighAl / Fe-rich" by best fit alone; CRAMM
+   then re-arbitrates that attribution with the pixel's fitted 2.2 µm
+   absorption center against per-rule calibrated wavelength windows
+   (`absorption_center_range`) — the spectroscopically meaningful axis along
+   which these four subtypes are actually defined. See *Enhancements over
+   USGS MICA → Wavelength-based muscovite attribution*.
+3. **From mineral detection to mineral composition.** Beyond labeling
+   muscovite pixels, CRAMM fits the per-pixel 2.2 µm absorption-center
+   wavelength (`mus_center`) — a quantitative composition proxy whose
+   thermodynamic basis (Tschermak substitution vs. wv2200 on a
+   GEMS/MINES23.1 reaction-path phase diagram) lets each fitted pixel be
+   read as muscovite chemistry, formation temperature and fluid K⁺/H⁺
+   conditions. See *Application: reading muscovite composition from
+   mus_center*.
+
+Everything is pure Python and GUI-free. Cross-platform:
+**Windows / Linux / macOS** · Python **3.9 – 3.13**
+
+---
+
+## Highlights
+
+- **Enhanced MICA pipeline** — continuum removal → closed-form 2×2 least
+  squares → fit (r²) & absorption depth → five-layer constraint filtering
+  **+ the CRAMM depth-ratio constraint**, driven by a JSON rule library
+  (77 rules covering clay, sulfate, carbonate, mica, chlorite, amphibole,
+  iron oxide, snow/ice and their mixtures).
+- **Quantitative muscovite mapping** — per-pixel 2.2 µm absorption-center
+  wavelength as a dedicated thematic map and float array; the same center
+  also re-arbitrates the lowAl / medAl / medhighAl / Fe-rich attribution
+  against calibrated wavelength windows, with a phase-diagram
+  interpretation framework.
+- **Whole-scene and single-spectrum modes** — batch-classify an entire scene
+  to GeoTIFF, or identify one spectrum (GUI point-click, field
+  spectrometer) with Top-N ranking and a PDF diagnostic report.
+- **Sensor-agnostic core** — everything downstream of data loading consumes a
+  generic `(spectrum, wavelengths, FWHM, valid bands)` contract. The bundled
+  reader covers EMIT L2A NetCDF; any other sensor (airborne or spaceborne)
+  plugs in through the same seven-tuple — no rule or code changes needed.
+- **Fast** — reference-side constants are precompiled once per band
+  configuration (two-level cache; ~16× speedup on repeated single-spectrum
+  calls), and scene classification parallelizes across rules with worker
+  processes.
+- **Bit-exact discipline** — serial and parallel paths produce identical
+  bytes; every change is guarded by a dual-path golden regression suite.
+- **Self-contained** — the rule library (`rf.json`), the USGS `splib06b`
+  spectral library, and the mineral color table are bundled inside the wheel.
+
+## How it works
+
+```
+Hyperspectral reflectance cube (any VNIR–SWIR sensor)
+      │  built-in: load_emit (EMIT L2A NetCDF, bad-band removal)
+      │  or your own loader → (spectrum, wl, w, bp, chanels)
+      ▼
+Reference resampling ── splib06b records ──► sensor wavelengths/FWHM
+      │                                        (Gaussian kernel, cached)
+      ▼
+Per-rule evaluation (77 rules, parallel across rules)
+      │  diagnostic features: continuum removal → 2×2 LSQ → r² / depth
+      │  not-absorption / not-related features: exclusion filters
+      │  continuum & depth-ratio constraints
+      ▼
+Best-match selection (argmax fit×depth)  +  muscovite 2.2 µm center fit
+      │
+      ▼
+Wavelength-arbitrated muscovite subtyping
+      │  mus_center vs. per-rule absorption_center_range windows
+      │  (lowAl / medAl / medhighAl / Fe-rich re-attribution)
+      ▼
+Mineral map · color-enhanced map · muscovite map (+ raw float arrays)
+```
+
+## Installation
+
+```bash
+pip install cramm            # core features (PyPI wheels on all three platforms)
+pip install cramm[tiff]      # + GeoTIFF output (GDAL; PyPI wheels are Windows-only)
+pip install cramm[pdf]       # + single-spectrum feature PDF diagnostics
+pip install cramm[all]       # everything
+```
+
+**GDAL on Linux/macOS**: PyPI ships GDAL wheels for Windows only. Install a
+system libgdal first (conda-forge recommended), then install without deps:
+
+```bash
+conda install -c conda-forge gdal
+pip install cramm --no-deps        # or: pip install cramm[pdf]
+```
+
+Without GDAL, only `write_tiff` (GeoTIFF output) is unavailable — all
+classification and analysis functions work (lazy import).
+
+From source (sdist / checkout):
+
+```bash
+pip install .            # add [all] for the optional extras
+```
+
+## Quick start
+
+### Command line
+
+The CLI uses the built-in EMIT L2A reader; for other sensors, use the Python
+API (below) with your own loader.
+
+```bash
+cramm -i EMIT_L2A_RFL_001_xxx.nc -o output [-n scene] [-w 4] [--raw]
+```
+
+| Flag | Default | Meaning |
+|---|---|---|
+| `-i`, `--input` | *(required)* | Path to the EMIT L2A NetCDF file |
+| `-o`, `--output` | `.` | Output directory |
+| `-n`, `--name` | input filename | Output filename prefix |
+| `-w`, `--workers` | `min(cpu, 8)` | Parallel worker processes (`1` = serial) |
+| `--raw` | off | Also save `mus_center` + `fd` float arrays as `.npz` |
+
+**Output files** (written to `<output>/<name>*`):
+
+| File | Content |
+|---|---|
+| `<name>_mapping_orth.tiff` | Mineral map (orthorectified, rule-library colors) |
+| `<name>_color_enhanced_orth.tiff` | Color-enhanced mineral map |
+| `<name>_mus_orth.tiff` | Muscovite 2.2 µm absorption-center thematic map |
+| `<name>_raw.npz` | *(only with `--raw`)* `mus_center` [μm] + `fd` (fit×depth), float `[r, c]` |
+
+### Python API
+
+```python
+from cramm import MicaEngine
+
+engine = MicaEngine()                                    # all resources bundled
+spectrum, lon, lat, w, bp, wl, chanels = engine.load_emit("EMIT_xxx.nc")
+
+# --- whole scene → GeoTIFF -------------------------------------------------
+orth, color, mus = engine.spectrum_analysis(spectrum, wl, w, bp, chanels,
+                                            n_workers=4)
+engine.write_tiff("output/scene", lon, lat, orth, color, mus)
+
+# --- single spectrum (one pixel, field spectrometer, ...) ------------------
+pixel = spectrum[100, 200, :]                            # full-band [285] or selected [len(chanels)]
+results = engine.classify_spectrum(pixel, wl, w, bp, chanels,
+                                   top_n=5, pdf_path="diag.pdf")
+for r in results:
+    print(f"{r['name']:50s} fit={r['fit']:.4f}  fd={r['fd']:.4f}")
+```
+
+### Other sensors (non-EMIT data)
+
+`load_emit` is only a convenience reader. For any other sensor, load the cube
+yourself and pass the same band-configuration contract — references are
+resampled to your wavelengths/FWHM automatically:
+
+```python
+from cramm import MicaEngine
+import numpy as np
+
+engine = MicaEngine()
+spectrum = my_loader("scene.dat")          # [rows, cols, bands] reflectance
+w  = np.array([...])                       # band center wavelengths [µm]
+bp = np.array([...])                       # band FWHM [µm]
+chanels = np.arange(len(w))                # valid bands (drop bad-band indices)
+wl = w[chanels]
+
+orth, color, mus = engine.spectrum_analysis(spectrum, wl, w, bp, chanels,
+                                            n_workers=4)
+```
+
+Only the map rendering (`write_tiff`) needs geolocation (`lon`/`lat` grids);
+classification itself is purely spectral and location-free.
+
+`classify_spectrum` returns a list of `{"name", "fit", "fd"}` dicts sorted by
+descending fit (empty list when nothing passes the filters). With
+`pdf_path=` it also writes a multi-page PDF: one page per Top-N mineral with
+continuum-removed feature overlays and constraint annotations (requires the
+`[pdf]` extra).
+
+Each PDF page dissects one candidate rule — every diagnostic / not-absorption
+/ not-relative feature with its continuum endpoints, the reference
+continuum-removed profile (squares) against the input (circles), and the
+full constraint audit (k0/k1, r², raw depth, weights, thresholds):
+
+![Single-spectrum diagnostic PDF: per-rule feature dissection](docs/single_spectrum_diagnostic.png)
+
+More scenarios — float (`raw=True`) output, custom rule libraries, the
+`invalidate_caches()` contract, component-level calls — in
+[example_usage.py](https://github.com/leecugb/cramm/blob/main/example_usage.py): `python example_usage.py pixel`.
+
+## API overview
+
+| `MicaEngine` method | Purpose |
+|---|---|
+| `load_emit(path)` | *(EMIT-specific convenience reader)* Read EMIT L2A NetCDF → `(spectrum, lon, lat, w, bp, wl, chanels)`; float32 cube, bad bands removed, fill values zeroed. Not needed for other sensors — supply the same tuple yourself |
+| `spectrum_analysis(spectrum, wl, w, bp, chanels, ...)` | Classify a whole scene → 3 uint8 RGB images; `raw=True` adds `mus_center` + `fd` float arrays. Supports `progress_callback`, `log_callback`, `cancel_flag`, `n_workers` |
+| `classify_spectrum(spectrum, wl, w, bp, chanels, top_n=10, pdf_path=None)` | Identify one spectrum → Top-N `[{"name", "fit", "fd"}]` |
+| `write_tiff(prefix, lon, lat, orth, color, mus)` | Orthorectify (pyresample) and write the 3 GeoTIFFs; requires GDAL |
+| `get_resample(w, bp)` | All reference spectra resampled to the sensor bands `{record_id: spectrum}` (cached) |
+| `invalidate_caches()` | **Required** after mutating `engine.rf` in place — see below |
+
+### Custom rule libraries
+
+```python
+engine = MicaEngine(rf_path="my_rules.json")          # at construction
+# — or mutate in place —
+engine.rf["my_mineral"] = {...}
+engine.invalidate_caches()                            # mandatory!
+```
+
+The compiled-rule cache is keyed on band configuration only, **not** on rule
+content. If you modify `engine.rf` after any classification call, you must call
+`invalidate_caches()` (or build a new engine) — otherwise results silently use
+the old reference-side constants.
+
+## Enhancements over USGS MICA
+
+CRAMM extends the original USGS MICA decision rules with an optional per-rule
+**secondary-feature depth-ratio constraint**,
+`max_depth_ratio_feat1_over_feat0`:
+
+> After the standard MICA filtering, a rule carrying this key rejects any pixel
+> where `raw_depth(feat1) / raw_depth(feat0) ≥ threshold`, using the
+> *unweighted* feature depths `(1 − min(continuum-removed)) × k0`. Pixels with
+> an invalid primary feature (NaN depth) are conservatively kept.
+
+For white micas the primary 2.2 µm Al-OH absorption (feat0) must dominate the
+secondary ~2.35 µm feature (feat1); a secondary absorption that is too deep
+relative to the primary indicates look-alike minerals rather than muscovite /
+illite. Nine bundled rules use this constraint:
+
+| Threshold | Rules |
+|---|---|
+| `0.6` | muscovite_lowAl, muscovite_medAl, muscovite_medhighAl, muscovite_Fe-rich, illite_imt1, illite_gds4 |
+| `0.4` | kaolinite.5+muscoviteMedAl.5, kaolinite.5+muscoviteMedhighAl.5, kaolinite+muscovite_mix_intimate |
+
+The constraint is part of the rule schema — custom rule libraries can set
+`"max_depth_ratio_feat1_over_feat0": <float>` on any rule with ≥2 diagnostic
+features; omitting the key disables it (original MICA behavior).
+
+### Wavelength-based muscovite attribution
+
+CRAMM also adds an optional per-feature **absorption-center window**,
+`absorption_center_range` on a rule's first diagnostic feature. After the
+best-match selection, pixels attributed to a rule carrying this field are
+re-arbitrated by their fitted 2.2 µm absorption center (`mus_center`):
+
+> If the center falls inside exactly one rule's `[lo, hi)` window, differs
+> from the current match, and that rule itself accepted the pixel, the pixel
+> is reassigned to the matching rule (fit/depth/index follow, and the center
+> is refitted once with the new rule's endpoints). An invalid center, a
+> center outside every window, or a center inside several overlapping
+> windows keeps the original match (conservative).
+
+The four bundled pure-muscovite rules carry calibrated windows (anchored on
+each reference spectrum's measured wv2200): medhighAl `[2.195, 2.200)`,
+medAl `[2.200, 2.206)`, lowAl / Fe-rich `[2.206, 2.220)` — the latter two
+share a window, so wavelength never overrides their mutual attribution.
+This is a scene-classification feature; single-spectrum Top-N ranking is
+unaffected. Custom rule libraries opt in by adding the field; rules without
+it are never reassigned.
+
+## Application: reading muscovite composition from mus_center
+
+The muscovite thematic map's per-pixel `mus_center` (2.2 µm Al-OH absorption
+position) is a quantitative proxy for muscovite chemistry. The phase diagram
+below — a GEMS/MINES23.1 titration reaction-path model of the
+K₂O–Al₂O₃–SiO₂–H₂O–HCl–FeO–MgO system — overlays the Tschermak substitution
+degree X_Ts = X(Fe-Celadonite)+X(Celadonite) in the muscovite stability field
+with the corresponding wv2200 position (USGS conversion chain:
+X_Ts → Al₂O₃ wt% → λ = −3.1·Al₂O₃ + 2308):
+
+![Tschermak substitution degree vs. wv2200 in the muscovite field](docs/muscovite_wv2200_phase_diagram.png)
+
+X_Ts rises from ~0 on the high-T / low-K⁺ side to 0.35+ on the low-T / high-K⁺
+side, and the wv2200 contours (magenta, 2190→2215 nm) run nearly parallel to
+the X_Ts contours (dark blue). Each `mus_center` value fitted from an image
+pixel therefore maps directly onto this diagram, inverting muscovite
+composition — and with it formation temperature and fluid K⁺/H⁺ conditions —
+from orbit.
+
+## Performance notes
+
+- **Precompiled rules**: continuum endpoints, band indices, the reference-side
+  normal-equation constant `B` and depth factors are computed once per
+  `(wavelengths, FWHM, valid-band)` configuration and reused across all pixels
+  and calls.
+- **Parallelism**: scene classification fans out across the 77 rules with
+  `multiprocessing` (spawn context); BLAS is pinned to a single thread so the
+  parallel path stays bit-identical to the serial one.
+- **Typical runtime**: a full scene (e.g. an EMIT granule, ≈1280×1242 pixels)
+  classifies in about a minute with a few workers on a desktop; a warm
+  single-spectrum call is ≈10 ms.
+
+## Testing
+
+```bash
+python tests/test_core.py              # 18 API contract / behavior tests
+                                       # (integration section auto-skips without the test scene)
+python tests/test_custom_rules.py      # custom rule-library verification (7 scenarios:
+                                       #   rf_path / constraint & window edits / new rules / cache contract)
+python tests/test_parallel_isolation.py # shared-state isolation (6 checks: worker/thread
+                                       #   isolation, env restore, temp-file cleanup)
+
+# The suites below need the EMIT test scene in the working directory
+# (file name defined in each script's NC constant):
+python tests/check_rows_logic.py       # rows alive-pixel semantics (16 checks)
+python tests/test_single_spectrum.py   # single-spectrum identification (7 tests:
+                                       #   self-ID / noise robustness / determinism / ...)
+python tests/check_compiled_path.py    # compiled vs direct path, 302 pixels × 77 rules, bit-level diff
+python tests/test_parallel.py 4        # full-scene golden regression (parallel)
+python tests/test_parallel.py 1        # full-scene golden regression (serial)
+```
+
+**The golden baseline is platform-bound.** `tests/golden_arrays.npz` encodes
+this machine's BLAS results; ulp-level differences across BLAS builds are
+expected. On a new platform — or after an intentional classification-semantics
+change — regenerate the baseline locally with `python regen_golden.py` (runs
+both paths, asserts serial ≡ parallel, then rewrites the golden) before
+relying on `test_parallel.py`.
+
+## Troubleshooting
+
+- **`netCDF4` fails to open a path containing non-ASCII characters on
+  Windows** — a limitation of the netCDF C library, not of CRAMM. `cd` into the
+  data directory and use a relative path instead.
+- **`ImportError: gdal`** — you called `write_tiff` without GDAL installed; see
+  *Installation*. Classification itself never imports GDAL.
+
+## Package layout
+
+```
+cramm/
+  __init__.py       # exports MicaEngine / ProcessResult
+  mica_engine.py    # facade: resource loading + component wiring + CLI main()
+  emit_reader.py    # EMIT L2A NetCDF reader + bad-band removal (float32 contract)
+  classifier.py     # MICA core: resampling / compiled rules / serial & parallel classification
+  renderer.py       # rendering: three maps / GeoTIFF / single-spectrum PDF diagnostics
+  data/             # rf.json + splib06b + color_table.json
+tests/              # bit-exact verification suite + API contract tests
+example_usage.py    # five usage-scenario examples
+```
+
+## Requirements
+
+- Python 3.9 – 3.13
+- Runtime: `numpy`, `pandas`, `netCDF4`, `pyproj`, `pyresample`, `threadpoolctl`
+- Optional: `gdal` (GeoTIFF), `matplotlib` (PDF diagnostics)
+
+## Acknowledgments
+
+The decision rules implement the USGS MICA system
+(Kokaly et al., `russet`-era rule set); reference spectra come from the USGS
+splib06b spectral library (Clark et al., 2007). The bundled test scene uses
+EMIT L2A products, courtesy of NASA/JPL.

cramm-1.0.0/CRAMM.egg-info/SOURCES.txt

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+LICENSE
+MANIFEST.in
+README.md
+benchmark.py
+example_usage.py
+pyproject.toml
+regen_golden.py
+CRAMM.egg-info/PKG-INFO
+CRAMM.egg-info/SOURCES.txt
+CRAMM.egg-info/dependency_links.txt
+CRAMM.egg-info/entry_points.txt
+CRAMM.egg-info/requires.txt
+CRAMM.egg-info/top_level.txt
+cramm/__init__.py
+cramm/classifier.py
+cramm/emit_reader.py
+cramm/mica_engine.py
+cramm/renderer.py
+cramm/data/color_table.json
+cramm/data/rf.json
+cramm/data/splib06b
+docs/muscovite_wv2200_phase_diagram.png
+docs/single_spectrum_diagnostic.png
+tests/check_compiled_path.py
+tests/check_rows_logic.py
+tests/golden_arrays.npz
+tests/test_core.py
+tests/test_custom_rules.py
+tests/test_parallel.py
+tests/test_parallel_isolation.py
+tests/test_single_spectrum.py

cramm-1.0.0/CRAMM.egg-info/dependency_links.txt

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+

cramm-1.0.0/CRAMM.egg-info/entry_points.txt

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+[console_scripts]
+cramm = cramm.mica_engine:main

cramm-1.0.0/CRAMM.egg-info/requires.txt

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+numpy
+pandas
+netCDF4
+pyproj
+pyresample
+threadpoolctl
+
+[all]
+gdal
+matplotlib
+
+[pdf]
+matplotlib
+
+[test]
+pytest
+matplotlib
+
+[tiff]
+gdal

cramm-1.0.0/CRAMM.egg-info/top_level.txt

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+cramm

cramm-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Shijie Li
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

cramm-1.0.0/MANIFEST.in

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+# sdist also ships tests and examples (the wheel contains only the cramm package)
+include README.md
+include example_usage.py
+include regen_golden.py
+include benchmark.py
+recursive-include tests *.py *.npz
+recursive-include docs *.png