risforge 0.1.0__tar.gz

risforge-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Amyr
+
+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.

risforge-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: risforge
+Version: 0.1.0
+Summary: Clean, deduplicate, and enrich RIS bibliographic files for systematic reviews.
+Author-email: Amyr <amyrhexa@gmail.com>
+License: MIT
+Project-URL: Homepage, https://github.com/amyr/risforge
+Project-URL: Repository, https://github.com/amyr/risforge
+Project-URL: Issues, https://github.com/amyr/risforge/issues
+Project-URL: Changelog, https://github.com/amyr/risforge/blob/main/CHANGELOG.md
+Keywords: ris,bibliography,systematic-review,deduplication,crossref,openalex,citation-management,prisma
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Text Processing :: Filters
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+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: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: rispy>=0.9.0
+Requires-Dist: requests>=2.31
+Requires-Dist: requests-cache>=1.1
+Requires-Dist: urllib3>=2.0
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0; extra == "dev"
+Requires-Dist: pytest-cov>=5.0; extra == "dev"
+Requires-Dist: build>=1.2; extra == "dev"
+Requires-Dist: twine>=5.0; extra == "dev"
+Dynamic: license-file
+
+# risforge
+
+**Clean, deduplicate, and enrich RIS bibliographic files for systematic reviews.**
+
+`risforge` takes a raw `.ris` export from Scopus, Web of Science, PubMed,
+EndNote, or any other reference manager and:
+
+1. **Cleans & deduplicates** it — normalizing titles, DOIs, and author
+   names, then clustering duplicate records (by exact DOI, and by a
+   title + first-author fallback) and merging each cluster into one
+   complete, data-loss-free record.
+2. **Enriches** it — filling in missing abstracts, journal names,
+   volumes/issues/pages, ISSNs, keywords, and open-access PDF links by
+   querying [Crossref](https://www.crossref.org/), [OpenAlex](https://openalex.org/),
+   [Semantic Scholar](https://www.semanticscholar.org/), and
+   [Unpaywall](https://unpaywall.org/). Existing fields are never
+   overwritten — only gaps are filled.
+
+It's built for the kind of unglamorous but essential prep work that
+comes before title/abstract screening in a systematic review: getting
+one clean, complete, deduplicated `.ris` file out of a pile of messy,
+overlapping database exports.
+
+## Features
+
+- **DOI-first deduplication** with a normalized title + first-author
+  fallback for records that lack a DOI, using union-find clustering so
+  transitively-linked duplicates across three, four, or more sources
+  all collapse into one record.
+- **Zero data loss on merge** — the most complete record in a
+  duplicate cluster is used as the base, and every other record in the
+  cluster supplements it with whatever fields it's missing.
+- **Non-destructive enrichment** — only empty fields are filled;
+  anything you (or an upstream export) already populated is left
+  alone.
+- **Resilient HTTP** — automatic retries with exponential backoff on
+  429/5xx responses, and a 7-day on-disk response cache so re-running
+  a pipeline doesn't re-hit the same APIs for records you've already
+  enriched.
+- **Library or CLI** — use it as `import risforge` in a script/notebook,
+  or as a single `risforge` command.
+
+## Installation
+
+```bash
+pip install risforge
+```
+
+Requires Python 3.10+.
+
+## Quick start
+
+### Command line
+
+```bash
+# Clean and deduplicate only
+risforge clean raw_export.ris clean.ris
+
+# Enrich an already-clean file
+risforge enrich clean.ris enriched.ris --email you@example.com
+
+# Both steps in one call
+risforge pipeline raw_export.ris --email you@example.com
+```
+
+The `pipeline` subcommand writes `<input>_clean.ris` and
+`<input>_enriched.ris` next to your input file by default; pass
+`--dedup-output` / `--output` to control that explicitly.
+
+An email address is required by Crossref, OpenAlex, and Unpaywall's
+"polite pool" usage policies — it's sent as a contact address in your
+requests, never stored or transmitted anywhere else.
+
+### Python API
+
+```python
+from risforge import clean_ris_file, RisEnricher, run_pipeline
+
+# Clean + deduplicate only
+records, errors = clean_ris_file("raw_export.ris", "clean.ris")
+print(f"{len(records)} unique records, {len(errors)} parse errors")
+
+# Enrich only
+enricher = RisEnricher(email="you@example.com")
+stats = enricher.enrich_file("clean.ris", "enriched.ris")
+print(f"Enriched {stats['enriched']}/{stats['processed']} records")
+
+# Both, in one call
+result = run_pipeline(
+    input_path="raw_export.ris",
+    dedup_path="clean.ris",
+    enriched_path="enriched.ris",
+    email="you@example.com",
+)
+print(result.cleaned_record_count, result.enrichment_stats)
+```
+
+## Configuration
+
+`RisEnricher` accepts a few constructor arguments beyond `email`:
+
+```python
+RisEnricher(
+    email="you@example.com",
+    cache_name=".api_cache",   # base filename for the on-disk HTTP cache
+    session=None,              # inject your own requests.Session (mainly for testing)
+)
+```
+
+`enrich_file()` also accepts `fail_report_path` (where unresolved-DOI
+records are written as JSON) and `request_delay_seconds` (delay
+between records; defaults to 0.1s to stay within provider rate limits).
+
+## Troubleshooting
+
+- **"Unresolved DOI via Title Matching" in the failure report** — the
+  record had no DOI and its title didn't match any Crossref result
+  above the 90% similarity threshold closely enough to resolve one.
+  These records are returned unmodified rather than guessed at.
+- **Enrichment seems slow** — each record makes up to 5 API calls
+  (1 for DOI resolution if needed, 4 for metadata) with a small delay
+  between records. Re-running against the same input is fast, since
+  responses are cached for 7 days.
+- **A field I already had got left alone even though enrichment "ran"** —
+  that's intentional. Enrichment only fills empty fields; it never
+  overwrites existing data.
+
+## Contributing
+
+1. Clone the repo and install in editable mode with dev dependencies:
+   ```bash
+   pip install -e ".[dev]"
+   ```
+2. Run the test suite:
+   ```bash
+   pytest
+   ```
+3. Open a PR. Please include tests for any behavioral change, and note
+   any deduplication/merge/enrichment logic changes explicitly in
+   `CHANGELOG.md` — this package's core value is *predictability* for
+   systematic review workflows, so silent behavior changes are treated
+   as bugs.
+
+## License
+
+MIT — see [LICENSE](LICENSE).

risforge-0.1.0/README.md

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+# risforge
+
+**Clean, deduplicate, and enrich RIS bibliographic files for systematic reviews.**
+
+`risforge` takes a raw `.ris` export from Scopus, Web of Science, PubMed,
+EndNote, or any other reference manager and:
+
+1. **Cleans & deduplicates** it — normalizing titles, DOIs, and author
+   names, then clustering duplicate records (by exact DOI, and by a
+   title + first-author fallback) and merging each cluster into one
+   complete, data-loss-free record.
+2. **Enriches** it — filling in missing abstracts, journal names,
+   volumes/issues/pages, ISSNs, keywords, and open-access PDF links by
+   querying [Crossref](https://www.crossref.org/), [OpenAlex](https://openalex.org/),
+   [Semantic Scholar](https://www.semanticscholar.org/), and
+   [Unpaywall](https://unpaywall.org/). Existing fields are never
+   overwritten — only gaps are filled.
+
+It's built for the kind of unglamorous but essential prep work that
+comes before title/abstract screening in a systematic review: getting
+one clean, complete, deduplicated `.ris` file out of a pile of messy,
+overlapping database exports.
+
+## Features
+
+- **DOI-first deduplication** with a normalized title + first-author
+  fallback for records that lack a DOI, using union-find clustering so
+  transitively-linked duplicates across three, four, or more sources
+  all collapse into one record.
+- **Zero data loss on merge** — the most complete record in a
+  duplicate cluster is used as the base, and every other record in the
+  cluster supplements it with whatever fields it's missing.
+- **Non-destructive enrichment** — only empty fields are filled;
+  anything you (or an upstream export) already populated is left
+  alone.
+- **Resilient HTTP** — automatic retries with exponential backoff on
+  429/5xx responses, and a 7-day on-disk response cache so re-running
+  a pipeline doesn't re-hit the same APIs for records you've already
+  enriched.
+- **Library or CLI** — use it as `import risforge` in a script/notebook,
+  or as a single `risforge` command.
+
+## Installation
+
+```bash
+pip install risforge
+```
+
+Requires Python 3.10+.
+
+## Quick start
+
+### Command line
+
+```bash
+# Clean and deduplicate only
+risforge clean raw_export.ris clean.ris
+
+# Enrich an already-clean file
+risforge enrich clean.ris enriched.ris --email you@example.com
+
+# Both steps in one call
+risforge pipeline raw_export.ris --email you@example.com
+```
+
+The `pipeline` subcommand writes `<input>_clean.ris` and
+`<input>_enriched.ris` next to your input file by default; pass
+`--dedup-output` / `--output` to control that explicitly.
+
+An email address is required by Crossref, OpenAlex, and Unpaywall's
+"polite pool" usage policies — it's sent as a contact address in your
+requests, never stored or transmitted anywhere else.
+
+### Python API
+
+```python
+from risforge import clean_ris_file, RisEnricher, run_pipeline
+
+# Clean + deduplicate only
+records, errors = clean_ris_file("raw_export.ris", "clean.ris")
+print(f"{len(records)} unique records, {len(errors)} parse errors")
+
+# Enrich only
+enricher = RisEnricher(email="you@example.com")
+stats = enricher.enrich_file("clean.ris", "enriched.ris")
+print(f"Enriched {stats['enriched']}/{stats['processed']} records")
+
+# Both, in one call
+result = run_pipeline(
+    input_path="raw_export.ris",
+    dedup_path="clean.ris",
+    enriched_path="enriched.ris",
+    email="you@example.com",
+)
+print(result.cleaned_record_count, result.enrichment_stats)
+```
+
+## Configuration
+
+`RisEnricher` accepts a few constructor arguments beyond `email`:
+
+```python
+RisEnricher(
+    email="you@example.com",
+    cache_name=".api_cache",   # base filename for the on-disk HTTP cache
+    session=None,              # inject your own requests.Session (mainly for testing)
+)
+```
+
+`enrich_file()` also accepts `fail_report_path` (where unresolved-DOI
+records are written as JSON) and `request_delay_seconds` (delay
+between records; defaults to 0.1s to stay within provider rate limits).
+
+## Troubleshooting
+
+- **"Unresolved DOI via Title Matching" in the failure report** — the
+  record had no DOI and its title didn't match any Crossref result
+  above the 90% similarity threshold closely enough to resolve one.
+  These records are returned unmodified rather than guessed at.
+- **Enrichment seems slow** — each record makes up to 5 API calls
+  (1 for DOI resolution if needed, 4 for metadata) with a small delay
+  between records. Re-running against the same input is fast, since
+  responses are cached for 7 days.
+- **A field I already had got left alone even though enrichment "ran"** —
+  that's intentional. Enrichment only fills empty fields; it never
+  overwrites existing data.
+
+## Contributing
+
+1. Clone the repo and install in editable mode with dev dependencies:
+   ```bash
+   pip install -e ".[dev]"
+   ```
+2. Run the test suite:
+   ```bash
+   pytest
+   ```
+3. Open a PR. Please include tests for any behavioral change, and note
+   any deduplication/merge/enrichment logic changes explicitly in
+   `CHANGELOG.md` — this package's core value is *predictability* for
+   systematic review workflows, so silent behavior changes are treated
+   as bugs.
+
+## License
+
+MIT — see [LICENSE](LICENSE).

risforge-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=68.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "risforge"
+version = "0.1.0"
+description = "Clean, deduplicate, and enrich RIS bibliographic files for systematic reviews."
+readme = "README.md"
+requires-python = ">=3.10"
+license = { text = "MIT" }
+authors = [
+    { name = "Amyr", email = "amyrhexa@gmail.com" }
+]
+keywords = [
+    "ris",
+    "bibliography",
+    "systematic-review",
+    "deduplication",
+    "crossref",
+    "openalex",
+    "citation-management",
+    "prisma",
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Text Processing :: Filters",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Operating System :: OS Independent",
+]
+
+dependencies = [
+    "rispy>=0.9.0",
+    "requests>=2.31",
+    "requests-cache>=1.1",
+    "urllib3>=2.0",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=8.0",
+    "pytest-cov>=5.0",
+    "build>=1.2",
+    "twine>=5.0",
+]
+
+[project.urls]
+Homepage = "https://github.com/amyr/risforge"
+Repository = "https://github.com/amyr/risforge"
+Issues = "https://github.com/amyr/risforge/issues"
+Changelog = "https://github.com/amyr/risforge/blob/main/CHANGELOG.md"
+
+[project.scripts]
+risforge = "risforge.cli:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-dir]
+"" = "src"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]

risforge-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

risforge-0.1.0/src/risforge/__init__.py

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+"""risforge: clean, deduplicate, and enrich RIS bibliographic files.
+
+Typical usage::
+
+    from risforge import clean_ris_file, RisEnricher, run_pipeline
+
+    # Clean + deduplicate only
+    records, errors = clean_ris_file("raw.ris", "clean.ris")
+
+    # Enrich only
+    enricher = RisEnricher(email="you@example.com")
+    stats = enricher.enrich_file("clean.ris", "enriched.ris")
+
+    # Both, in one call
+    result = run_pipeline(
+        "raw.ris", "clean.ris", "enriched.ris", email="you@example.com"
+    )
+
+See the ``risforge`` console script (``risforge --help``) for the
+equivalent command-line interface.
+"""
+
+from risforge.cleaning import clean_ris_file, process_ris_file
+from risforge.enrichment import RisEnricher
+from risforge.exceptions import RisForgeError, RisParsingError
+from risforge.pipeline import PipelineResult, run_pipeline
+
+__version__ = "0.1.0"
+
+__all__ = [
+    "clean_ris_file",
+    "process_ris_file",
+    "RisEnricher",
+    "run_pipeline",
+    "PipelineResult",
+    "RisForgeError",
+    "RisParsingError",
+]