openbionews 0.4.0__tar.gz

openbionews-0.4.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to OpenBioNews are documented here. The format is loosely
+based on [Keep a Changelog](https://keepachangelog.com/), and the project aims
+to follow [Semantic Versioning](https://semver.org/).
+
+## [Unreleased]
+
+## [0.4.0]
+
+### Added
+- **LLM as a labelled interpretation layer** — with per-sentence citations now
+  the factual body, an enabled LLM (Ollama / OpenAI-compatible) no longer writes
+  the facts; it adds only a clearly-marked *"💡 Why it matters (AI analysis)"*
+  note beneath the deterministic cited claims (turn on `output.why_it_matters`).
+  The facts stay verbatim and cited — nothing to hallucinate — while the model
+  supplies interpretation you can tell apart at a glance. A failed note is dropped
+  with a warning; the cited body always renders. Runs across Markdown/HTML/text/RSS.
+- **Change detection between runs** — OpenBioNews now remembers each item's
+  salient state (by NCT id, recall number, EDGAR accession) and flags what
+  *changed* on the next run: a trial moved to Terminated, results posted, a recall
+  reclassified. Changed stories are boosted in ranking and badged (`🔔 Status:
+  Recruiting → Terminated`). Deterministic — a literal state comparison, **no LLM**.
+  New `openbionews/history.py`; state lives in `digest/state.json` (configurable).
+- **Thematic groups** (`sources.THEMES`) — one-tap watch-list seeds that cut
+  across diseases by *modality / approach / company cohort*: **AI in drug
+  discovery**, **New Approach Methodologies (NAM)**, gene & cell therapy, CRISPR,
+  mRNA, ADCs, radiopharmaceuticals, GLP-1/obesity, psychedelics, longevity. Each
+  seeds search terms and a lead-sponsor cohort. Wizard multi-select + web chips.
+- **Stackable web filters** — chips on the hosted page now *add* to a field
+  instead of replacing it, and multi-value fields become a ClinicalTrials.gov
+  `OR` query, so you can watch several conditions / companies / themes at once.
+- **Per-sentence citations** — every sentence of a story's brief is bound to the
+  primary-source record it was lifted from, rendered as a numbered `[n]` / `<sup>`
+  marker with a keyed source list beneath. Fully deterministic: the text is
+  verbatim from the cited record, so there is nothing to hallucinate and **no LLM
+  is involved**. Applies across every output (Markdown, HTML, text, RSS) and the
+  hosted web page. New `openbionews/cite.py`; a `Claim` model on each cluster.
+- Continuous integration (GitHub Actions) running the test suite on Linux, macOS
+  and Windows across Python 3.9–3.12, plus an install/CLI smoke test.
+- Community health files: `CONTRIBUTING.md`, `CODE_OF_CONDUCT.md`, issue and pull
+  request templates.
+- **Offline mixed demo**: `openbionews run --demo` now builds a digest from
+  bundled samples covering trade-press RSS *and* all three primary sources
+  (ClinicalTrials.gov, FDA recalls, SEC filings), each with a source citation —
+  a network-free preview of the real output.
+- **RSS feed output** (`--format rss`, or `output.format: rss`): writes a valid
+  RSS 2.0 feed (`digest/latest.xml`) you can subscribe to in any reader, with a
+  source citation in every item. Standard-library only. (Closes #2.)
+- **openFDA drug-approvals connector** (`connectors.openfda_approvals`): recent
+  Drugs@FDA approvals — original and supplemental (new indication) — cited to
+  the Drugs@FDA page. Wizard toggle, doctor check, and demo coverage included.
+  (Closes #1.)
+- **Therapeutic-area presets** (oncology, cardiometabolic, rare disease,
+  neurology, immunology, infectious disease): one-tap watch-list seeding in the
+  setup wizard and matching chips on the hosted page. (Closes #4.)
+- **openFDA drug-shortages connector** (`connectors.openfda_shortages`): current
+  (or resolved) shortages by drug/company, cited to the FDA Drug Shortages
+  database — completing the FDA trio (recalls + approvals + shortages).
+- **Hosted page parity**: the web app now has five tabs — Clinical trials, FDA
+  recalls, **FDA approvals**, **FDA shortages**, and SEC filings — matching the
+  CLI's source coverage, all client-side with shareable links.
+
+### Fixed
+- Windows: the setup wizard and `doctor` could raise `UnicodeEncodeError` when
+  invoked directly (bypassing the CLI entry point) because stdout defaulted to a
+  legacy code page. The UTF-8 guard is now shared and applied at every entry
+  point (`openbionews/termio.py`). Caught by the new cross-platform CI.
+- De-duplication now keys on an item's stable id (NCT id, recall number, EDGAR
+  accession) before its link. Previously, sources whose links differ only by a
+  query string (e.g. openFDA recall records) could be wrongly collapsed into one.
+
+## [0.3.0]
+
+### Added
+- **openFDA drug-recalls connector** — enforcement reports filtered by
+  firm/product/reason, classification and report-date recency; cites the FDA
+  record.
+- **SEC EDGAR connector** — full-text search of filings by company/drug/term,
+  form type and filed-within recency; cites the filing document and sets the
+  contact `User-Agent` SEC requires. Runs server-side, avoiding browser CORS.
+- Hosted web page gained an **SEC filings tab** (with a graceful fallback to
+  SEC's own EDGAR search when a browser blocks the request) and an **FDA drug
+  recalls tab**, plus shareable filter links.
+- Useful filters based on how biopharma teams monitor: trial recency +
+  industry-sponsored-only; recall report-date recency + voluntary/mandated.
+
+## [0.2.0]
+
+### Added
+- **Primary-source model**: `connectors/` package and a **ClinicalTrials.gov**
+  connector with a shared watch list and per-story source citations.
+- Hosted, zero-install web page (`docs/`) for filtering ClinicalTrials.gov.
+
+## [0.1.0]
+
+### Added
+- Initial release: RSS/Atom digest with cross-outlet de-dup, importance ranking
+  and read-time; no-LLM / Ollama / OpenAI-compatible summaries; optional SMTP
+  email; onboarding wizard; `doctor` diagnostics; Markdown/HTML/text output.
+  Pure standard library, cross-platform, MIT-licensed.

openbionews-0.4.0/CODE_OF_CONDUCT.md

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+# Code of Conduct
+
+## Our pledge
+
+We as members, contributors, and maintainers pledge to make participation in
+OpenBioNews a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+## Our standards
+
+Examples of behavior that contributes to a positive environment:
+
+- Being respectful of differing opinions, viewpoints, and experiences
+- Giving and gracefully accepting constructive feedback
+- Focusing on what is best for the community
+- Showing empathy toward other people
+
+Examples of unacceptable behavior:
+
+- Harassment, insults, or derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement
+
+Maintainers are responsible for clarifying and enforcing these standards and
+will take appropriate and fair corrective action in response to any behavior
+they deem inappropriate, threatening, offensive, or harmful.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by opening a confidential issue or contacting a maintainer. All
+complaints will be reviewed and investigated promptly and fairly.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1.
+
+[homepage]: https://www.contributor-covenant.org

openbionews-0.4.0/CONTRIBUTING.md

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+# Contributing to OpenBioNews
+
+Thanks for helping build a free, self-hosted news tool. Contributions of every
+size are welcome — a typo fix, a new feed, a whole new connector.
+
+## Ground rules
+
+- **Zero required dependencies.** The core runs on the Python standard library
+  (3.9+). Don't add a runtime dependency without discussion; optional extras go
+  under `[project.optional-dependencies]`.
+- **Privacy first.** The tool must never phone home. No telemetry, no analytics.
+- **Everything works offline where it can.** Failures degrade gracefully — a
+  dead feed is skipped, a failed LLM call falls back to no-LLM.
+
+## Getting started
+
+```bash
+git clone https://github.com/fedor-i/OpenBioNews.git
+cd OpenBioNews
+python3 -m openbionews run --demo     # works offline, no install
+pip install .                          # optional: install the CLI
+```
+
+## Running the tests
+
+The suite uses only the standard library, so no install is needed:
+
+```bash
+python3 tests/test_pipeline.py         # prints ok/FAIL per test
+# or, if you have pytest:
+pytest
+```
+
+CI runs these on Linux, macOS and Windows across Python 3.9–3.12. Please make
+sure `python3 tests/test_pipeline.py` passes before opening a PR.
+
+## Adding a primary-source connector
+
+Connectors are the highest-value contributions. See
+[`ARCHITECTURE.md`](ARCHITECTURE.md) → *Adding a primary-source connector*. In
+short:
+
+1. Add `openbionews/connectors/<name>.py` with a class extending
+   `connectors.base.Connector`, a `fetch()` and an `available()`.
+2. **Split parsing from fetching** (a `parse_*` function) so it can be tested
+   with a fixture and no network.
+3. Attach a `Citation` to every `Item` and set `age_exempt=True`.
+4. Register it in `connectors/__init__.py`, add a config block in `config.py`,
+   and a step in `setup_wizard.py`.
+5. Add fixture-based tests.
+
+## Adding feeds
+
+Edit the bundles in `openbionews/sources.py`. Prefer official or well-known
+RSS/Atom feeds, and run `openbionews doctor` to confirm the URL resolves.
+
+## Style
+
+- Match the surrounding code; keep functions small and documented.
+- Prefer clarity over cleverness. Comment *why*, not *what*.
+- Keep user-facing text plain and active-voice.
+
+## Pull requests
+
+- One focused change per PR.
+- Update `CHANGELOG.md` under "Unreleased".
+- Describe what changed and how you tested it.
+
+By contributing, you agree your work is licensed under the project's
+[MIT License](LICENSE).

openbionews-0.4.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 OpenBioNews contributors
+
+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.

openbionews-0.4.0/MANIFEST.in

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+include README.md
+include LICENSE
+include CHANGELOG.md
+include CONTRIBUTING.md
+include CODE_OF_CONDUCT.md
+include config.example.json
+include requirements.txt
+recursive-include openbionews/data *.xml *.json
+recursive-include tests *.py