sciwrite-lint 0.2.1__tar.gz → 0.2.2__tar.gz

{sciwrite_lint-0.2.1/sciwrite_lint.egg-info → sciwrite_lint-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sciwrite-lint
-Version: 0.2.1
+Version: 0.2.2
 Summary: A linter for scientific manuscripts — reference verification, consistency checking, and structural validation.
 Author: Sergey Samsonau
 Maintainer-email: Authentic Research Partners LLC <info@arpconnect.com>
@@ -9,6 +9,7 @@ Project-URL: Homepage, https://arpconnect.com
 Project-URL: Repository, https://github.com/authentic-research-partners/sciwrite-lint
 Project-URL: Documentation, https://github.com/authentic-research-partners/sciwrite-lint#readme
 Project-URL: Issues, https://github.com/authentic-research-partners/sciwrite-lint/issues
+Project-URL: Paper, https://arxiv.org/abs/2604.08501
 Keywords: linter,latex,bibtex,pdf,scientific-writing,academic-writing,citation-checker,reference-verification,claim-verification,manuscript,peer-review,arxiv,vllm,qwen
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Developers
@@ -51,6 +52,8 @@ Dynamic: license-file
 
 # sciwrite-lint
 
+[![arXiv](https://img.shields.io/badge/arXiv-2604.08501-b31b1b.svg)](https://arxiv.org/abs/2604.08501)
+
 A linter for scientific manuscripts. Checks that your references exist, your metadata is accurate, your citations support the claims you make, and your cited papers' own bibliographies are real. Works on LaTeX and PDF. Runs entirely on your machine. Produces a **SciLint Score**.
 
 The only open-source tool that combines reference verification, claim checking, manuscript consistency, figure analysis, and bibliography verification in one pipeline — powered entirely by a local LLM on your own GPU.
@@ -154,6 +157,32 @@ uv tool install sciwrite-lint --python 3.13
 
 uv downloads Python 3.13 automatically (does not affect any Python you may already have) and installs sciwrite-lint as a globally available command.
 
+### Reproducible environment (optional)
+
+`pyproject.toml` declares lower bounds for dependencies, so `uv tool install` / `pip install` may resolve newer versions as upstream releases ship. If you want the exact versions the maintainer develops and tests against — for reproducing benchmarks, debugging version-drift issues, or CI — install from [`requirements-pinned.txt`](requirements-pinned.txt) instead.
+
+**What's in it:** top-level packages declared in `pyproject.toml` pinned to `==` versions. Transitive dependencies are not pinned — pip resolves them within each top-level package's own constraints. This is a deliberate middle ground: it locks the packages sciwrite-lint actually imports and tests against, without over-constraining the dep tree.
+
+```bash
+# Clone the public repo (required — uv tool install can't read a local file)
+git clone https://github.com/authentic-research-partners/sciwrite-lint.git
+cd sciwrite-lint
+
+# With uv (recommended — fast, isolated, manages Python itself)
+uv venv --python 3.13 .venv
+source .venv/bin/activate
+uv pip install -r requirements-pinned.txt
+uv pip install -e . --no-deps    # install sciwrite-lint source; deps already pinned
+
+# Or with plain pip
+python3.13 -m venv .venv
+source .venv/bin/activate
+pip install -r requirements-pinned.txt
+pip install -e . --no-deps
+```
+
+Activate the venv in each new terminal with `source .venv/bin/activate`. For most users, the plain `uv tool install sciwrite-lint` above is simpler — use the pinned file only when you need exact version reproduction.
+
 ## Setup
 
 ```bash
@@ -167,7 +196,18 @@ sciwrite-lint containers monitor       # live dashboard: service health, VRAM, K
 
 `init` detects `.tex` files and their `.bib` references and generates a `.sciwrite-lint.toml` config. Review to confirm the right files were detected.
 
-**Paywalled references:** drop PDFs into `local_pdfs/` with filenames matching the reference title. The tool fuzzy-matches filenames against your `.bib` titles and uses local copies instead of downloading.
+**Providing PDFs manually (`local_pdfs/`):** Drop any reference PDF into the `local_pdfs/` directory to skip the download step entirely. This is useful when you already have the file, when the paper is paywalled, or when the publisher blocks automated downloads (Cell, Springer, some PMC pages). Name files by the reference title:
+
+```
+local_pdfs/
+├── States of Curiosity Modulate Hippocampus-Dependent Learning.pdf
+├── Mind in Society.pdf
+└── The System of Professions.pdf
+```
+
+The tool fuzzy-matches filenames against your `.bib` titles (threshold 0.80) and copies matches to the workspace. On the next run, matched references upgrade from T2 to T1 and go through GROBID parsing and claim verification like any other full-text reference.
+
+**Finding what to download:** `sciwrite-lint verify` lists T2 references that are confirmed open access with direct URLs — open in your browser and save to `local_pdfs/`. For paywalled papers, use your institution's library access.
 
 **Optional API keys** increase rate limits for Semantic Scholar, NCBI, and CORE:
 
@@ -269,6 +309,21 @@ For contributors and advanced users:
 - [docs/evals.md](https://github.com/authentic-research-partners/sciwrite-lint/blob/main/docs/evals.md) — detection evaluation framework, adding test cases
 - [docs/calibration.md](https://github.com/authentic-research-partners/sciwrite-lint/blob/main/docs/calibration.md) — SciLint Score calibration against ground-truth papers
 
+## Citation
+
+If you use sciwrite-lint in your research, please cite the accompanying paper ([arXiv:2604.08501](https://arxiv.org/abs/2604.08501)):
+
+```bibtex
+@article{samsonau2026sciwritelint,
+  title   = {sciwrite-lint: Verification Infrastructure for the Age of Science Vibe-Writing},
+  author  = {Samsonau, Sergey V.},
+  journal = {arXiv preprint arXiv:2604.08501},
+  year    = {2026},
+}
+```
+
+GitHub's "Cite this repository" button (powered by [`CITATION.cff`](CITATION.cff)) will also generate this for you.
+
 ## License
 
 MIT

{sciwrite_lint-0.2.1 → sciwrite_lint-0.2.2}/README.md

@@ -1,5 +1,7 @@
 # sciwrite-lint
 
+[![arXiv](https://img.shields.io/badge/arXiv-2604.08501-b31b1b.svg)](https://arxiv.org/abs/2604.08501)
+
 A linter for scientific manuscripts. Checks that your references exist, your metadata is accurate, your citations support the claims you make, and your cited papers' own bibliographies are real. Works on LaTeX and PDF. Runs entirely on your machine. Produces a **SciLint Score**.
 
 The only open-source tool that combines reference verification, claim checking, manuscript consistency, figure analysis, and bibliography verification in one pipeline — powered entirely by a local LLM on your own GPU.
@@ -103,6 +105,32 @@ uv tool install sciwrite-lint --python 3.13
 
 uv downloads Python 3.13 automatically (does not affect any Python you may already have) and installs sciwrite-lint as a globally available command.
 
+### Reproducible environment (optional)
+
+`pyproject.toml` declares lower bounds for dependencies, so `uv tool install` / `pip install` may resolve newer versions as upstream releases ship. If you want the exact versions the maintainer develops and tests against — for reproducing benchmarks, debugging version-drift issues, or CI — install from [`requirements-pinned.txt`](requirements-pinned.txt) instead.
+
+**What's in it:** top-level packages declared in `pyproject.toml` pinned to `==` versions. Transitive dependencies are not pinned — pip resolves them within each top-level package's own constraints. This is a deliberate middle ground: it locks the packages sciwrite-lint actually imports and tests against, without over-constraining the dep tree.
+
+```bash
+# Clone the public repo (required — uv tool install can't read a local file)
+git clone https://github.com/authentic-research-partners/sciwrite-lint.git
+cd sciwrite-lint
+
+# With uv (recommended — fast, isolated, manages Python itself)
+uv venv --python 3.13 .venv
+source .venv/bin/activate
+uv pip install -r requirements-pinned.txt
+uv pip install -e . --no-deps    # install sciwrite-lint source; deps already pinned
+
+# Or with plain pip
+python3.13 -m venv .venv
+source .venv/bin/activate
+pip install -r requirements-pinned.txt
+pip install -e . --no-deps
+```
+
+Activate the venv in each new terminal with `source .venv/bin/activate`. For most users, the plain `uv tool install sciwrite-lint` above is simpler — use the pinned file only when you need exact version reproduction.
+
 ## Setup
 
 ```bash
@@ -116,7 +144,18 @@ sciwrite-lint containers monitor       # live dashboard: service health, VRAM, K
 
 `init` detects `.tex` files and their `.bib` references and generates a `.sciwrite-lint.toml` config. Review to confirm the right files were detected.
 
-**Paywalled references:** drop PDFs into `local_pdfs/` with filenames matching the reference title. The tool fuzzy-matches filenames against your `.bib` titles and uses local copies instead of downloading.
+**Providing PDFs manually (`local_pdfs/`):** Drop any reference PDF into the `local_pdfs/` directory to skip the download step entirely. This is useful when you already have the file, when the paper is paywalled, or when the publisher blocks automated downloads (Cell, Springer, some PMC pages). Name files by the reference title:
+
+```
+local_pdfs/
+├── States of Curiosity Modulate Hippocampus-Dependent Learning.pdf
+├── Mind in Society.pdf
+└── The System of Professions.pdf
+```
+
+The tool fuzzy-matches filenames against your `.bib` titles (threshold 0.80) and copies matches to the workspace. On the next run, matched references upgrade from T2 to T1 and go through GROBID parsing and claim verification like any other full-text reference.
+
+**Finding what to download:** `sciwrite-lint verify` lists T2 references that are confirmed open access with direct URLs — open in your browser and save to `local_pdfs/`. For paywalled papers, use your institution's library access.
 
 **Optional API keys** increase rate limits for Semantic Scholar, NCBI, and CORE:
 
@@ -218,6 +257,21 @@ For contributors and advanced users:
 - [docs/evals.md](https://github.com/authentic-research-partners/sciwrite-lint/blob/main/docs/evals.md) — detection evaluation framework, adding test cases
 - [docs/calibration.md](https://github.com/authentic-research-partners/sciwrite-lint/blob/main/docs/calibration.md) — SciLint Score calibration against ground-truth papers
 
+## Citation
+
+If you use sciwrite-lint in your research, please cite the accompanying paper ([arXiv:2604.08501](https://arxiv.org/abs/2604.08501)):
+
+```bibtex
+@article{samsonau2026sciwritelint,
+  title   = {sciwrite-lint: Verification Infrastructure for the Age of Science Vibe-Writing},
+  author  = {Samsonau, Sergey V.},
+  journal = {arXiv preprint arXiv:2604.08501},
+  year    = {2026},
+}
+```
+
+GitHub's "Cite this repository" button (powered by [`CITATION.cff`](CITATION.cff)) will also generate this for you.
+
 ## License
 
 MIT

{sciwrite_lint-0.2.1 → sciwrite_lint-0.2.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "sciwrite-lint"
-version = "0.2.1"
+version = "0.2.2"
 description = "A linter for scientific manuscripts — reference verification, consistency checking, and structural validation."
 requires-python = ">=3.13,<3.14"
 license = "MIT"
@@ -53,6 +53,7 @@ Homepage = "https://arpconnect.com"
 Repository = "https://github.com/authentic-research-partners/sciwrite-lint"
 Documentation = "https://github.com/authentic-research-partners/sciwrite-lint#readme"
 Issues = "https://github.com/authentic-research-partners/sciwrite-lint/issues"
+Paper = "https://arxiv.org/abs/2604.08501"
 
 [project.optional-dependencies]
 dev = [

{sciwrite_lint-0.2.1 → sciwrite_lint-0.2.2}/sciwrite_lint/__init__.py

@@ -1,3 +1,3 @@
 """sciwrite-lint: a linter for scientific manuscripts."""
 
-__version__ = "0.2.1"
+__version__ = "0.2.2"

{sciwrite_lint-0.2.1 → sciwrite_lint-0.2.2}/sciwrite_lint/cli/fetch.py

@@ -123,6 +123,12 @@ def fetch_for_citations(
                     except Exception as e:
                         logger.warning(f"{c.key}: parse skipped: {e}")
             elif result.url:
+                if result.is_oa:
+                    meta.access["is_oa"] = True
+                if result.oa_url:
+                    meta.access["oa_url"] = result.oa_url
+                if result.is_oa or result.oa_url:
+                    save_metadata(meta, refs_dir)
                 logger.warning(f"{c.key}: manual download needed: {result.url}")
             else:
                 logger.warning(f"{c.key}: no source found")

{sciwrite_lint-0.2.1 → sciwrite_lint-0.2.2}/sciwrite_lint/cli/verify.py

@@ -8,7 +8,32 @@ from pathlib import Path
 
 from loguru import logger
 
-from sciwrite_lint.models import CheckResult, Finding
+from sciwrite_lint.models import CheckResult, Citation, CitationMetadata, Finding
+
+
+def classify_t2_refs(
+    citations: list[Citation],
+    all_meta: dict[str, CitationMetadata],
+) -> tuple[list[tuple[str, str]], list[tuple[str, str]]]:
+    """Split T2 refs into OA (manual download) and other (no source).
+
+    Returns (t2_oa, t2_other) where each is a list of (key, url_or_reason).
+    """
+    t2_oa: list[tuple[str, str]] = []
+    t2_other: list[tuple[str, str]] = []
+    for c in sorted(citations, key=lambda x: x.key):
+        meta = all_meta.get(c.key)
+        if not meta:
+            continue
+        tier = meta.access.get("tier", "NC")
+        if tier == "T2":
+            if meta.access.get("is_oa") and meta.access.get("oa_url"):
+                t2_oa.append((c.key, meta.access["oa_url"]))
+            else:
+                reason = meta.access.get("acquisition_reason", "")
+                if reason:
+                    t2_other.append((c.key, reason))
+    return t2_oa, t2_other
 
 
 _TIER_MARKERS = {
@@ -205,21 +230,18 @@ def run_status(args: argparse.Namespace) -> int:
     print("  T2 = verified, no full text (confirmed real)")
     print("  T3 = not found in APIs or dead URL")
 
-    # Show acquisition reasons for T2 refs
-    t2_reasons: list[tuple[str, str]] = []
-    for c in sorted(citations, key=lambda x: x.key):
-        meta = all_meta.get(c.key)
-        if not meta:
-            continue
-        tier = meta.access.get("tier", "NC")
-        if tier == "T2":
-            reason = meta.access.get("acquisition_reason", "")
-            if reason:
-                t2_reasons.append((c.key, reason))
-    if t2_reasons:
+    # Show T2 refs split by OA status
+    t2_oa, t2_other = classify_t2_refs(citations, all_meta)
+    if t2_oa:
+        print()
+        print("  T2 open access — manual download needed:")
+        print("  (download PDF, save to local_pdfs/ by title)")
+        for key, url in t2_oa:
+            print(f"    {key}: {url}")
+    if t2_other:
         print()
         print("  T2 acquisition details:")
-        for key, reason in t2_reasons:
+        for key, reason in t2_other:
             print(f"    {key}: {reason}")
 
     return 0

{sciwrite_lint-0.2.1 → sciwrite_lint-0.2.2}/sciwrite_lint/fulltext.py

@@ -122,6 +122,8 @@ class AcquisitionResult(BaseModel):
     url: str | None = None
     abstract: str | None = None
     reason: str = ""
+    is_oa: bool = False
+    oa_url: str | None = None
 
 
 # ---------------------------------------------------------------------------
@@ -788,10 +790,18 @@ async def acquire_fulltext(
             if progress:
                 print(" not found")
 
-    # 9. Suggest manual download
+    # 9. Determine OA status and suggest manual download
     combined_reason = (
         "; ".join(failed_sources) if failed_sources else "no sources available"
     )
+    # OA confirmed by Unpaywall or OpenAlex
+    known_oa = bool(uw_data) or bool(oa_url)
+    best_oa_url = None
+    if uw_data:
+        best_oa_url = uw_data.get("oa_url") or uw_data.get("pdf_url")
+    if not best_oa_url and oa_url:
+        best_oa_url = oa_url
+
     best_url = None
     if uw_data:
         best_url = uw_data.get("pdf_url") or uw_data.get("oa_url")
@@ -806,6 +816,8 @@ async def acquire_fulltext(
             url=best_url,
             abstract=core_abstract,
             reason=combined_reason,
+            is_oa=known_oa,
+            oa_url=best_oa_url,
         )
 
     return AcquisitionResult(

{sciwrite_lint-0.2.1 → sciwrite_lint-0.2.2}/sciwrite_lint/pipeline.py

@@ -1548,6 +1548,11 @@ async def _stage_fetch(
         elif not result.found:
             if result.reason:
                 meta.access["acquisition_reason"] = result.reason
+            if result.is_oa:
+                meta.access["is_oa"] = True
+            if result.oa_url:
+                meta.access["oa_url"] = result.oa_url
+            if result.reason or result.is_oa or result.oa_url:
                 save_metadata(meta, references_dir)
             logger.debug(
                 f"{c.key}: PDF not acquired (stays T2)"

{sciwrite_lint-0.2.1 → sciwrite_lint-0.2.2/sciwrite_lint.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sciwrite-lint
-Version: 0.2.1
+Version: 0.2.2
 Summary: A linter for scientific manuscripts — reference verification, consistency checking, and structural validation.
 Author: Sergey Samsonau
 Maintainer-email: Authentic Research Partners LLC <info@arpconnect.com>
@@ -9,6 +9,7 @@ Project-URL: Homepage, https://arpconnect.com
 Project-URL: Repository, https://github.com/authentic-research-partners/sciwrite-lint
 Project-URL: Documentation, https://github.com/authentic-research-partners/sciwrite-lint#readme
 Project-URL: Issues, https://github.com/authentic-research-partners/sciwrite-lint/issues
+Project-URL: Paper, https://arxiv.org/abs/2604.08501
 Keywords: linter,latex,bibtex,pdf,scientific-writing,academic-writing,citation-checker,reference-verification,claim-verification,manuscript,peer-review,arxiv,vllm,qwen
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Developers
@@ -51,6 +52,8 @@ Dynamic: license-file
 
 # sciwrite-lint
 
+[![arXiv](https://img.shields.io/badge/arXiv-2604.08501-b31b1b.svg)](https://arxiv.org/abs/2604.08501)
+
 A linter for scientific manuscripts. Checks that your references exist, your metadata is accurate, your citations support the claims you make, and your cited papers' own bibliographies are real. Works on LaTeX and PDF. Runs entirely on your machine. Produces a **SciLint Score**.
 
 The only open-source tool that combines reference verification, claim checking, manuscript consistency, figure analysis, and bibliography verification in one pipeline — powered entirely by a local LLM on your own GPU.
@@ -154,6 +157,32 @@ uv tool install sciwrite-lint --python 3.13
 
 uv downloads Python 3.13 automatically (does not affect any Python you may already have) and installs sciwrite-lint as a globally available command.
 
+### Reproducible environment (optional)
+
+`pyproject.toml` declares lower bounds for dependencies, so `uv tool install` / `pip install` may resolve newer versions as upstream releases ship. If you want the exact versions the maintainer develops and tests against — for reproducing benchmarks, debugging version-drift issues, or CI — install from [`requirements-pinned.txt`](requirements-pinned.txt) instead.
+
+**What's in it:** top-level packages declared in `pyproject.toml` pinned to `==` versions. Transitive dependencies are not pinned — pip resolves them within each top-level package's own constraints. This is a deliberate middle ground: it locks the packages sciwrite-lint actually imports and tests against, without over-constraining the dep tree.
+
+```bash
+# Clone the public repo (required — uv tool install can't read a local file)
+git clone https://github.com/authentic-research-partners/sciwrite-lint.git
+cd sciwrite-lint
+
+# With uv (recommended — fast, isolated, manages Python itself)
+uv venv --python 3.13 .venv
+source .venv/bin/activate
+uv pip install -r requirements-pinned.txt
+uv pip install -e . --no-deps    # install sciwrite-lint source; deps already pinned
+
+# Or with plain pip
+python3.13 -m venv .venv
+source .venv/bin/activate
+pip install -r requirements-pinned.txt
+pip install -e . --no-deps
+```
+
+Activate the venv in each new terminal with `source .venv/bin/activate`. For most users, the plain `uv tool install sciwrite-lint` above is simpler — use the pinned file only when you need exact version reproduction.
+
 ## Setup
 
 ```bash
@@ -167,7 +196,18 @@ sciwrite-lint containers monitor       # live dashboard: service health, VRAM, K
 
 `init` detects `.tex` files and their `.bib` references and generates a `.sciwrite-lint.toml` config. Review to confirm the right files were detected.
 
-**Paywalled references:** drop PDFs into `local_pdfs/` with filenames matching the reference title. The tool fuzzy-matches filenames against your `.bib` titles and uses local copies instead of downloading.
+**Providing PDFs manually (`local_pdfs/`):** Drop any reference PDF into the `local_pdfs/` directory to skip the download step entirely. This is useful when you already have the file, when the paper is paywalled, or when the publisher blocks automated downloads (Cell, Springer, some PMC pages). Name files by the reference title:
+
+```
+local_pdfs/
+├── States of Curiosity Modulate Hippocampus-Dependent Learning.pdf
+├── Mind in Society.pdf
+└── The System of Professions.pdf
+```
+
+The tool fuzzy-matches filenames against your `.bib` titles (threshold 0.80) and copies matches to the workspace. On the next run, matched references upgrade from T2 to T1 and go through GROBID parsing and claim verification like any other full-text reference.
+
+**Finding what to download:** `sciwrite-lint verify` lists T2 references that are confirmed open access with direct URLs — open in your browser and save to `local_pdfs/`. For paywalled papers, use your institution's library access.
 
 **Optional API keys** increase rate limits for Semantic Scholar, NCBI, and CORE:
 
@@ -269,6 +309,21 @@ For contributors and advanced users:
 - [docs/evals.md](https://github.com/authentic-research-partners/sciwrite-lint/blob/main/docs/evals.md) — detection evaluation framework, adding test cases
 - [docs/calibration.md](https://github.com/authentic-research-partners/sciwrite-lint/blob/main/docs/calibration.md) — SciLint Score calibration against ground-truth papers
 
+## Citation
+
+If you use sciwrite-lint in your research, please cite the accompanying paper ([arXiv:2604.08501](https://arxiv.org/abs/2604.08501)):
+
+```bibtex
+@article{samsonau2026sciwritelint,
+  title   = {sciwrite-lint: Verification Infrastructure for the Age of Science Vibe-Writing},
+  author  = {Samsonau, Sergey V.},
+  journal = {arXiv preprint arXiv:2604.08501},
+  year    = {2026},
+}
+```
+
+GitHub's "Cite this repository" button (powered by [`CITATION.cff`](CITATION.cff)) will also generate this for you.
+
 ## License
 
 MIT