fresh-cbm 0.2.0__tar.gz

fresh_cbm-0.2.0/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright 2026 UBC FRESH Lab
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

fresh_cbm-0.2.0/PKG-INFO

@@ -0,0 +1,117 @@
+Metadata-Version: 2.4
+Name: fresh-cbm
+Version: 0.2.0
+Summary: Exact cached libcbm stand-state tables for WS4/FEMIC carbon
+License-Expression: Apache-2.0
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.26
+Requires-Dist: pandas>=2.2
+Requires-Dist: pyarrow>=15
+Requires-Dist: jsonschema>=4.20
+Provides-Extra: test
+Requires-Dist: pytest>=8; extra == "test"
+Requires-Dist: pytest-cov>=5; extra == "test"
+Requires-Dist: numpydoc>=1.7; extra == "test"
+Requires-Dist: hypothesis>=6.100; extra == "test"
+Requires-Dist: types-jsonschema; extra == "test"
+Requires-Dist: pandas-stubs; extra == "test"
+Requires-Dist: ruff>=0.5; extra == "test"
+Requires-Dist: mypy>=1.10; extra == "test"
+Requires-Dist: build>=1.2; extra == "test"
+Dynamic: license-file
+
+# fresh-cbm
+
+Exact cached libcbm stand-state tables and lookup client for WS4/FEMIC carbon
+analyses.
+
+`fresh-cbm` stores the deterministic per-hectare carbon accounts produced by
+libcbm for a declared package and treatment family. Consumers can look up a
+stand state instead of rebuilding a CBM model for every analysis.
+
+## Documentation
+
+Published Sphinx site:
+
+https://ubc-fresh.github.io/fresh-cbm/
+
+Start with the cache format, building, and validation guides.
+
+## Status
+
+Phase P0 (workflow bootstrap and documentation) is complete. `ROADMAP.md` is the
+plan of record; P1 is planned.
+
+## Quick start
+
+```bash
+python -m pip install -e ".[test]"
+fresh-cbm-build --help
+fresh-cbm-validate --help
+fresh-cbm-package --help
+fresh-cbm-bench --help
+fresh-cbm-verify --help
+python -m pytest
+python scripts/dashboard.py
+sphinx-build -b html docs _build/html -W
+```
+
+The builder and validator require WS4 (`ws4[carbon]`). Pass `--ws4-path` or put
+the WS4 source root on `PYTHONPATH`; the client and tests do not.
+
+## Available cache
+
+`v0.1.0-tsa41` is the first published table:
+
+- 5,273 TSA41 track/age states
+- declared family: untreated + one `CC` event at offsets `0..49`
+- 50 years, 26 carbon accounts, float64
+- 2.85 GB
+- 55 release assets
+- validation: 102 sampled state/offset rows, max absolute error 0
+
+Release:
+https://github.com/UBC-FRESH/fresh-cbm/releases/tag/v0.1.0-tsa41
+
+`v0.1.0-tsa08` is the second package cache:
+
+- 3,761 TSA08 track/age states
+- untreated + `CC@0..49`
+- 50 years, 26 accounts, float64
+- 2.03 GB
+- build 2h05; validation 102 rows, max absolute error 0
+
+Release:
+https://github.com/UBC-FRESH/fresh-cbm/releases/tag/v0.1.0-tsa08
+
+## Benchmarks
+
+`fresh-cbm-bench` measures load, lookup, projection, and storage. On the published
+TSA41 cache, projection over 148,828 blocks took **2.33 s**; TSA08 over 371,565
+blocks took **4.96 s**. See `docs/guides/benchmarks.rst`.
+
+## How this project works
+
+This project follows the UBC-FRESH dev workflow. Work is planned as phases,
+tasks, and subtasks in `ROADMAP.md`, mirrored in GitHub issues, and recorded in
+`CHANGE_LOG.md`. The agent contract is `AGENTS.md`. Read `AGENTS.md` and
+`ROADMAP.md` before changing anything.
+
+## Repository map
+
+| Path | Purpose |
+| --- | --- |
+| `AGENTS.md` | Operating contract for coding agents |
+| `ROADMAP.md` | Plan of record and issue tracker map |
+| `CHANGE_LOG.md` | Dated narrative of changes |
+| `docs/` | Sphinx site, published to GitHub Pages |
+| `notes/` | Decisions and focused plans |
+| `fresh_cbm/` | Python client, manifest schema, family contract, and effect projection |
+| `scripts/` | Builder, validator, workflow validator, and dashboard |
+| `tests/` | pytest suite |
+
+## License
+
+Apache-2.0. See `LICENSE`.

fresh_cbm-0.2.0/README.md

@@ -0,0 +1,93 @@
+# fresh-cbm
+
+Exact cached libcbm stand-state tables and lookup client for WS4/FEMIC carbon
+analyses.
+
+`fresh-cbm` stores the deterministic per-hectare carbon accounts produced by
+libcbm for a declared package and treatment family. Consumers can look up a
+stand state instead of rebuilding a CBM model for every analysis.
+
+## Documentation
+
+Published Sphinx site:
+
+https://ubc-fresh.github.io/fresh-cbm/
+
+Start with the cache format, building, and validation guides.
+
+## Status
+
+Phase P0 (workflow bootstrap and documentation) is complete. `ROADMAP.md` is the
+plan of record; P1 is planned.
+
+## Quick start
+
+```bash
+python -m pip install -e ".[test]"
+fresh-cbm-build --help
+fresh-cbm-validate --help
+fresh-cbm-package --help
+fresh-cbm-bench --help
+fresh-cbm-verify --help
+python -m pytest
+python scripts/dashboard.py
+sphinx-build -b html docs _build/html -W
+```
+
+The builder and validator require WS4 (`ws4[carbon]`). Pass `--ws4-path` or put
+the WS4 source root on `PYTHONPATH`; the client and tests do not.
+
+## Available cache
+
+`v0.1.0-tsa41` is the first published table:
+
+- 5,273 TSA41 track/age states
+- declared family: untreated + one `CC` event at offsets `0..49`
+- 50 years, 26 carbon accounts, float64
+- 2.85 GB
+- 55 release assets
+- validation: 102 sampled state/offset rows, max absolute error 0
+
+Release:
+https://github.com/UBC-FRESH/fresh-cbm/releases/tag/v0.1.0-tsa41
+
+`v0.1.0-tsa08` is the second package cache:
+
+- 3,761 TSA08 track/age states
+- untreated + `CC@0..49`
+- 50 years, 26 accounts, float64
+- 2.03 GB
+- build 2h05; validation 102 rows, max absolute error 0
+
+Release:
+https://github.com/UBC-FRESH/fresh-cbm/releases/tag/v0.1.0-tsa08
+
+## Benchmarks
+
+`fresh-cbm-bench` measures load, lookup, projection, and storage. On the published
+TSA41 cache, projection over 148,828 blocks took **2.33 s**; TSA08 over 371,565
+blocks took **4.96 s**. See `docs/guides/benchmarks.rst`.
+
+## How this project works
+
+This project follows the UBC-FRESH dev workflow. Work is planned as phases,
+tasks, and subtasks in `ROADMAP.md`, mirrored in GitHub issues, and recorded in
+`CHANGE_LOG.md`. The agent contract is `AGENTS.md`. Read `AGENTS.md` and
+`ROADMAP.md` before changing anything.
+
+## Repository map
+
+| Path | Purpose |
+| --- | --- |
+| `AGENTS.md` | Operating contract for coding agents |
+| `ROADMAP.md` | Plan of record and issue tracker map |
+| `CHANGE_LOG.md` | Dated narrative of changes |
+| `docs/` | Sphinx site, published to GitHub Pages |
+| `notes/` | Decisions and focused plans |
+| `fresh_cbm/` | Python client, manifest schema, family contract, and effect projection |
+| `scripts/` | Builder, validator, workflow validator, and dashboard |
+| `tests/` | pytest suite |
+
+## License
+
+Apache-2.0. See `LICENSE`.

fresh_cbm-0.2.0/fresh_cbm/__init__.py

@@ -0,0 +1,237 @@
+"""Exact libcbm stand-state cache client."""
+
+from __future__ import annotations
+
+import hashlib
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Any, cast
+
+import numpy as np
+import pandas as pd
+
+from .family import ChainFamily
+from .schema import load_manifest
+
+
+@dataclass(frozen=True)
+class StateCache:
+    """A loaded exact stand-state table.
+
+    Parameters
+    ----------
+    root : pathlib.Path
+        Cache directory containing ``manifest.json``, ``index.parquet``, and
+        ``values/``.
+    manifest : dict
+        Parsed manifest.
+    index : pandas.DataFrame
+        State index in row order.
+    """
+
+    root: Path
+    manifest: dict[str, Any]
+    index: pd.DataFrame
+
+    @classmethod
+    def load(cls, root: str | Path, *, validate: bool = True) -> StateCache:
+        """Load a cache directory.
+
+        Parameters
+        ----------
+        root : path-like
+            Cache directory.
+        validate : bool, optional
+            Check the index, file set, and array shapes. Defaults to True.
+
+        Returns
+        -------
+        StateCache
+            The loaded cache.
+        """
+        path = Path(root)
+        manifest = load_manifest(path / "manifest.json")
+        index = pd.read_parquet(path / "index.parquet")
+        cache = cls(root=path, manifest=manifest, index=index)
+        if validate:
+            cache.validate()
+        return cache
+
+    def validate(self) -> None:
+        """Check the index, file set, offsets, and array shapes.
+
+        Raises
+        ------
+        ValueError
+            When the cache is incomplete or inconsistent with its manifest.
+        """
+        required = {"state_id", "track_id", "track_name", "age"}
+        missing = required - set(self.index.columns)
+        if missing:
+            raise ValueError(f"cache index is missing columns: {sorted(missing)}")
+        states = int(self.manifest["states"])
+        if len(self.index) != states:
+            raise ValueError(f"cache index has {len(self.index)} rows but manifest says {states}")
+        years = self.years
+        accounts = len(self.accounts)
+        expected = (states, years + 1, accounts)
+        family = self.chain_family
+        offsets = self.manifest["offsets"]
+        if not isinstance(offsets, list):
+            raise ValueError("manifest offsets must be a list")
+        if family is not None:
+            if tuple(int(value) for value in offsets) != family.offsets:
+                raise ValueError("chain_family offsets do not match manifest offsets")
+            if bool(self.manifest["empty"]) != family.allow_empty:
+                raise ValueError("chain_family empty policy does not match manifest")
+        files = self.manifest["files"]
+        if not isinstance(files, list):
+            raise ValueError("manifest files must be a list")
+        for name in files:
+            if not isinstance(name, str):
+                raise ValueError("manifest file names must be strings")
+            path = self.root / name
+            if not path.is_file():
+                raise ValueError(f"cache file is missing: {name}")
+            array = np.load(path, mmap_mode="r")
+            if array.shape != expected:
+                raise ValueError(f"{name} has shape {array.shape}; expected {expected}")
+
+    def verify_checksums(self, path: str | Path | None = None) -> None:
+        """Verify files against a SHA256SUMS manifest.
+
+        Parameters
+        ----------
+        path : path-like or None, optional
+            Checksum file. Defaults to ``SHA256SUMS`` in the cache root.
+
+        Raises
+        ------
+        ValueError
+            When a file is missing or a digest does not match.
+        """
+        source = Path(path) if path is not None else self.root / "SHA256SUMS"
+        if not source.is_file():
+            raise ValueError(f"checksum file is missing: {source}")
+        for line in source.read_text(encoding="utf-8").splitlines():
+            if not line.strip():
+                continue
+            digest, name = line.split("  ", 1)
+            target = self.root / name
+            if not target.is_file():
+                raise ValueError(f"checksum target is missing: {name}")
+            actual = hashlib.sha256(target.read_bytes()).hexdigest()
+            if actual != digest:
+                raise ValueError(f"checksum mismatch: {name}")
+
+    @property
+    def chain_family(self) -> ChainFamily | None:
+        """Return the declared chain family, if the manifest has one.
+
+        Returns
+        -------
+        ChainFamily or None
+            The family record, or None for a legacy manifest without one.
+        """
+        raw = self.manifest.get("chain_family")
+        return None if raw is None else ChainFamily.from_manifest(raw)
+
+    @property
+    def accounts(self) -> tuple[str, ...]:
+        """Return the cached account names."""
+        values = self.manifest["accounts"]
+        if not isinstance(values, list):
+            raise ValueError("manifest accounts must be a list")
+        return tuple(str(value) for value in values)
+
+    @property
+    def years(self) -> int:
+        """Return the stored horizon length in years."""
+        return int(self.manifest["years"])
+
+    def _row(self, track_id: int, age: int) -> int:
+        """Return the index row for a track and age."""
+        rows = self.index
+        match = rows[
+            (rows["track_id"].astype(int) == int(track_id)) & (rows["age"].astype(int) == int(age))
+        ]
+        if len(match) != 1:
+            raise KeyError(f"state not in cache: track={track_id} age={age}")
+        return int(match.iloc[0]["state_id"])
+
+    def array(self, chain_offset: int = -1) -> np.ndarray:
+        """Return the memmapped values for one chain offset.
+
+        Parameters
+        ----------
+        chain_offset : int, optional
+            Single ``CC`` event offset; ``-1`` is untreated.
+
+        Returns
+        -------
+        numpy.ndarray
+            The cached values with shape ``(states, years + 1, accounts)``.
+        """
+        name = "empty.npy" if chain_offset < 0 else f"offset_{chain_offset:02d}.npy"
+        return cast(np.ndarray, np.load(self.root / "values" / name, mmap_mode="r"))
+
+    def lookup_state(self, state_id: int, chain_offset: int = -1) -> np.ndarray:
+        """Return one state's ``(years + 1, accounts)`` array.
+
+        Parameters
+        ----------
+        state_id : int
+            Row in ``index.parquet``.
+        chain_offset : int, optional
+            Single ``CC`` event offset; ``-1`` is untreated.
+
+        Returns
+        -------
+        numpy.ndarray
+            The cached accounts.
+        """
+        return np.asarray(self.array(chain_offset)[int(state_id)])
+
+    def lookup(self, track_id: int, age: int, chain_offset: int = -1) -> np.ndarray:
+        """Return one state's ``(years + 1, accounts)`` array.
+
+        Parameters
+        ----------
+        track_id : int
+            Dataset track id.
+        age : int
+            Initial stand age.
+        chain_offset : int, optional
+            Single ``CC`` event offset; ``-1`` is untreated.
+
+        Returns
+        -------
+        numpy.ndarray
+            The cached accounts.
+        """
+        return self.lookup_state(self._row(track_id, age), chain_offset)
+
+    def account(self, track_id: int, age: int, chain_offset: int, account: str) -> np.ndarray:
+        """Return one account series for a state.
+
+        Parameters
+        ----------
+        track_id : int
+            Dataset track id.
+        age : int
+            Initial stand age.
+        chain_offset : int
+            Single ``CC`` event offset; ``-1`` is untreated.
+        account : str
+            Account name.
+
+        Returns
+        -------
+        numpy.ndarray
+            The account values over all stored years.
+        """
+        try:
+            column = self.accounts.index(account)
+        except ValueError as exc:
+            raise KeyError(f"account not in cache: {account}") from exc
+        return self.lookup(track_id, age, chain_offset)[:, column]