sci-report-analyzer 1.0.0__tar.gz

sci_report_analyzer-1.0.0/LICENSE

@@ -0,0 +1,48 @@
+MIT License
+
+Copyright (c) 2026 Benjamin Piwowarski
+
+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.
+
+---------------------------------------------------------------------------
+
+THIRD-PARTY DATA
+
+The MIT license above covers VenueRank's *source code* only. The ranking
+datasets bundled under `source/data/` and fetched at runtime are the work of
+third parties and remain under their own terms:
+
+- Scimago Journal Rank (SJR) — © SCImago, derived from Scopus data, released
+  under Creative Commons Attribution-NonCommercial 3.0 (CC BY-NC 3.0).
+  Attribution required; commercial use is not permitted.
+  https://www.scimagojr.com/
+
+- CORE conference rankings — © Computing Research and Education Association of
+  Australasia (CORE). Publicly available for academic use; attribute CORE and
+  link back to the portal. https://portal.core.edu.au/conf-ranks/
+
+- Predatory-venue list — from the community-maintained
+  stop-predatory-journals project, distributed under the MIT License.
+  https://github.com/stop-predatory-journals/stop-predatory-journals.github.io
+
+JCR Impact Factors (Clarivate) are proprietary and are NEVER bundled or
+fetched; they are imported by the user at runtime and stay on the device.
+
+Because the bundled Scimago data is CC BY-NC, redistribution of VenueRank as a
+whole (code + bundled data) is limited to non-commercial use with attribution.

sci_report_analyzer-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: sci-report-analyzer
+Version: 1.0.0
+Summary: Track researchers' publications across sources and rank their venues, with per-person folders, notes and reports
+Author: Benjamin Piwowarski
+Author-email: Benjamin Piwowarski <benjamin@piwowarski.fr>
+License-Expression: MIT
+License-File: LICENSE
+Requires-Dist: alembic>=1.20.0
+Requires-Dist: beautifulsoup4>=4.15.0
+Requires-Dist: httpx>=0.28.1
+Requires-Dist: lark>=1.3.1
+Requires-Dist: latex2mathml>=3.81.1
+Requires-Dist: lxml>=6.1.3
+Requires-Dist: nicegui>=3.17.1
+Requires-Dist: pydantic>=2.13.5
+Requires-Dist: sqlalchemy>=2.1.1
+Requires-Python: >=3.13
+Description-Content-Type: text/markdown
+
+# SciReport Analyzer
+
+A local web app (NiceGUI + SQLite) to follow and evaluate researchers: it tracks their
+publications across sources, ranks their venues, and keeps per-person folders with tags,
+notes, stored PDFs and reports. Venues are ranked with Scimago, CORE (every edition since
+2008) and a predatory list.
+
+## Features
+
+- **People** with profiles on DBLP (SPARQL endpoint), HAL, ORCID, Semantic Scholar, Google
+  Scholar, theses.fr and OpenAlex (needs a free API key). Profiles are found automatically
+  and must be **validated** by hand; each source shows its update status (never synced,
+  updating, up to date, out of date, error). Syncing is on demand only.
+- **Merging** across sources (DOI, titles, years), preprints folded into the published
+  version, PDF links, manual split / merge / hide.
+- **Publications panel**: distribution, publications by year,
+  co-authors, author position, "with PhD student", cross-filtering, named **periods** with
+  **stars**, **flags** (short, demo…) that stick to papers, **tags** (global or within a
+  period) and Markdown **notes**, with a Markdown listing of the noted / tagged papers;
+  **tag from a pasted list** (e.g. a report's numbered list: matched by HAL id / DOI / title,
+  missing papers searched on HAL and added, the list's numbers kept for reporting).
+  Notes accept LaTeX (`$…$`, `$$…$$`), edited with a Markdown editor (toolbar, preview).
+- **Reports** within a period / folder: Markdown citing the papers (Pandoc's `[@key]`,
+  `@key`, `[@key]{.notes}`, `[@key]{.tags}`), checking each paper to discuss (by tags) is
+  cited, substituted (numbers like **#6**, titles, notes, tags) when copied.
+- **PDFs**: downloaded from the papers' open-access links (sources, else Unpaywall), one by
+  one or for all the papers shown, or uploaded; stored in the data directory and read in
+  the browser with PDF.js (highlight, text, drawing, images), the annotations saved back,
+  the paper's tags and notes alongside, bookmarks, the paper of a selected reference found
+  (or added from HAL); clean-up of the files of deleted papers.
+- **Documents** of a person within a folder / period (an application, a CV…): PDFs read and
+  annotated the same way, with bookmarks and a note; the person's papers they mention are
+  found (titles, DOIs / HAL ids, and the citations of numbered references like `[11]`),
+  marked, and show the paper's details next to the document; references can be linked by
+  hand from a selection; author-year citations (“(Lyu et al., 2023b)”) are linked too.
+- **Categories** per folder (an ordered tree, drag and drop, optional years): passages
+  selected in the PDFs are filed in them, listed per person, and inserted in reports as
+  Markdown.
+- **Venues** (Conferences / Journals pages): variants after cleaning, two-level
+  classification (kind → rank), default levels per kind, manual decisions per paper or per
+  venue that are never overridden.
+- Author highlighting: the person (with aliases) and their PhD students (from theses.fr),
+  with potential matches to confirm.
+- **Settings**: ranking sources, confidence threshold, rewrite and cleaning rules, venue
+  kinds, flags, datasets, JCR import, API keys, and **import / export** (replace, or merge
+  with per-conflict choices) to share them.
+
+## Usage
+
+```sh
+uv tool run sci-report-analyzer   # http://127.0.0.1:8081
+```
+
+or install it with `uv tool install sci-report-analyzer` and run `sci-report-analyzer`. Options:
+`--port`, `--host`, `--data-dir`, `--no-browser`. Press Ctrl-C, or the power button in the
+header, to quit.
+
+Data lives in `~/.local/share/sci-report-analyzer` (override with `SCI_REPORT_ANALYZER_DATA`). Your email is
+required before anything is fetched (it identifies you to the sources); it and the API keys can
+be given with `SCI_REPORT_ANALYZER_EMAIL`, `OPENALEX_API_KEY` / `S2_API_KEY` or in Settings → API keys.
+
+The database (not the PDFs) is backed up in `backups/` next to it: daily at startup (the last 7
+kept) and before each schema migration (`pre-migration-…`; a `.pending` marker next to one means
+that migration failed, and it is never removed). To restore a backup, stop the app and copy it
+over `sci-report-analyzer.sqlite` (removing the `-wal` / `-shm` files, if any).
+
+## Data sources
+
+Venue ranks come from third-party data, credited here and in the app (Settings → Data):
+
+- **[SCImago Journal & Country Rank](https://www.scimagojr.com)** (journals), downloaded
+  by the app from this repository (`datasets/journals.json`, checked every week). *SCImago, (n.d.). SJR — SCImago Journal & Country Rank [Portal].* SCImago allows
+  the use of its data as long as the source is cited; the journal metadata comes from
+  Scopus (Elsevier).
+- **[ICORE conference rankings](https://portal.core.edu.au/conf-ranks/)** (conferences,
+  every CORE edition since 2008), shipped with the app.
+- **Predatory list**: Beall's list as maintained by
+  [stop-predatory-journals](https://github.com/stop-predatory-journals/stop-predatory-journals.github.io)
+  (MIT licence), downloaded by the app and refreshed weekly. Being listed is an indication,
+  not a verdict.
+- **JCR** impact factors are Clarivate's and are not distributed: import your own export.
+
+See [`src/sci_report_analyzer/data/README.md`](src/sci_report_analyzer/data/README.md) for the
+files and their terms.
+
+## Licence
+
+The code is released under the [MIT licence](LICENSE). The ranking datasets keep their
+sources' terms (see above).
+
+## Development
+
+```sh
+uv sync
+uv run pre-commit install
+uv run pytest              # unit + simulated-UI tests
+uv run pytest -m live -o addopts=""   # smoke tests against the real APIs
+uv run sci-report-analyzer --live-reload  # offers a restart when the code changes
+```
+
+- `src/sci_report_analyzer/ranking/` — venue normalization, fuzzy matching and resolution
+  (checked against reference fixtures by `tests/test_matcher_parity.py`).
+- `sources/` — one adapter per source; `merge.py` — clustering; `sync.py` — syncing and
+  auto-matching; `venues.py` — venues; `pubview.py` — panel view model; `ui/` — pages.
+- Schema changes go through Alembic migrations (`db/migrations/versions`), applied at
+  startup; never edit a released migration.

sci_report_analyzer-1.0.0/README.md

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+# SciReport Analyzer
+
+A local web app (NiceGUI + SQLite) to follow and evaluate researchers: it tracks their
+publications across sources, ranks their venues, and keeps per-person folders with tags,
+notes, stored PDFs and reports. Venues are ranked with Scimago, CORE (every edition since
+2008) and a predatory list.
+
+## Features
+
+- **People** with profiles on DBLP (SPARQL endpoint), HAL, ORCID, Semantic Scholar, Google
+  Scholar, theses.fr and OpenAlex (needs a free API key). Profiles are found automatically
+  and must be **validated** by hand; each source shows its update status (never synced,
+  updating, up to date, out of date, error). Syncing is on demand only.
+- **Merging** across sources (DOI, titles, years), preprints folded into the published
+  version, PDF links, manual split / merge / hide.
+- **Publications panel**: distribution, publications by year,
+  co-authors, author position, "with PhD student", cross-filtering, named **periods** with
+  **stars**, **flags** (short, demo…) that stick to papers, **tags** (global or within a
+  period) and Markdown **notes**, with a Markdown listing of the noted / tagged papers;
+  **tag from a pasted list** (e.g. a report's numbered list: matched by HAL id / DOI / title,
+  missing papers searched on HAL and added, the list's numbers kept for reporting).
+  Notes accept LaTeX (`$…$`, `$$…$$`), edited with a Markdown editor (toolbar, preview).
+- **Reports** within a period / folder: Markdown citing the papers (Pandoc's `[@key]`,
+  `@key`, `[@key]{.notes}`, `[@key]{.tags}`), checking each paper to discuss (by tags) is
+  cited, substituted (numbers like **#6**, titles, notes, tags) when copied.
+- **PDFs**: downloaded from the papers' open-access links (sources, else Unpaywall), one by
+  one or for all the papers shown, or uploaded; stored in the data directory and read in
+  the browser with PDF.js (highlight, text, drawing, images), the annotations saved back,
+  the paper's tags and notes alongside, bookmarks, the paper of a selected reference found
+  (or added from HAL); clean-up of the files of deleted papers.
+- **Documents** of a person within a folder / period (an application, a CV…): PDFs read and
+  annotated the same way, with bookmarks and a note; the person's papers they mention are
+  found (titles, DOIs / HAL ids, and the citations of numbered references like `[11]`),
+  marked, and show the paper's details next to the document; references can be linked by
+  hand from a selection; author-year citations (“(Lyu et al., 2023b)”) are linked too.
+- **Categories** per folder (an ordered tree, drag and drop, optional years): passages
+  selected in the PDFs are filed in them, listed per person, and inserted in reports as
+  Markdown.
+- **Venues** (Conferences / Journals pages): variants after cleaning, two-level
+  classification (kind → rank), default levels per kind, manual decisions per paper or per
+  venue that are never overridden.
+- Author highlighting: the person (with aliases) and their PhD students (from theses.fr),
+  with potential matches to confirm.
+- **Settings**: ranking sources, confidence threshold, rewrite and cleaning rules, venue
+  kinds, flags, datasets, JCR import, API keys, and **import / export** (replace, or merge
+  with per-conflict choices) to share them.
+
+## Usage
+
+```sh
+uv tool run sci-report-analyzer   # http://127.0.0.1:8081
+```
+
+or install it with `uv tool install sci-report-analyzer` and run `sci-report-analyzer`. Options:
+`--port`, `--host`, `--data-dir`, `--no-browser`. Press Ctrl-C, or the power button in the
+header, to quit.
+
+Data lives in `~/.local/share/sci-report-analyzer` (override with `SCI_REPORT_ANALYZER_DATA`). Your email is
+required before anything is fetched (it identifies you to the sources); it and the API keys can
+be given with `SCI_REPORT_ANALYZER_EMAIL`, `OPENALEX_API_KEY` / `S2_API_KEY` or in Settings → API keys.
+
+The database (not the PDFs) is backed up in `backups/` next to it: daily at startup (the last 7
+kept) and before each schema migration (`pre-migration-…`; a `.pending` marker next to one means
+that migration failed, and it is never removed). To restore a backup, stop the app and copy it
+over `sci-report-analyzer.sqlite` (removing the `-wal` / `-shm` files, if any).
+
+## Data sources
+
+Venue ranks come from third-party data, credited here and in the app (Settings → Data):
+
+- **[SCImago Journal & Country Rank](https://www.scimagojr.com)** (journals), downloaded
+  by the app from this repository (`datasets/journals.json`, checked every week). *SCImago, (n.d.). SJR — SCImago Journal & Country Rank [Portal].* SCImago allows
+  the use of its data as long as the source is cited; the journal metadata comes from
+  Scopus (Elsevier).
+- **[ICORE conference rankings](https://portal.core.edu.au/conf-ranks/)** (conferences,
+  every CORE edition since 2008), shipped with the app.
+- **Predatory list**: Beall's list as maintained by
+  [stop-predatory-journals](https://github.com/stop-predatory-journals/stop-predatory-journals.github.io)
+  (MIT licence), downloaded by the app and refreshed weekly. Being listed is an indication,
+  not a verdict.
+- **JCR** impact factors are Clarivate's and are not distributed: import your own export.
+
+See [`src/sci_report_analyzer/data/README.md`](src/sci_report_analyzer/data/README.md) for the
+files and their terms.
+
+## Licence
+
+The code is released under the [MIT licence](LICENSE). The ranking datasets keep their
+sources' terms (see above).
+
+## Development
+
+```sh
+uv sync
+uv run pre-commit install
+uv run pytest              # unit + simulated-UI tests
+uv run pytest -m live -o addopts=""   # smoke tests against the real APIs
+uv run sci-report-analyzer --live-reload  # offers a restart when the code changes
+```
+
+- `src/sci_report_analyzer/ranking/` — venue normalization, fuzzy matching and resolution
+  (checked against reference fixtures by `tests/test_matcher_parity.py`).
+- `sources/` — one adapter per source; `merge.py` — clustering; `sync.py` — syncing and
+  auto-matching; `venues.py` — venues; `pubview.py` — panel view model; `ui/` — pages.
+- Schema changes go through Alembic migrations (`db/migrations/versions`), applied at
+  startup; never edit a released migration.

sci_report_analyzer-1.0.0/pyproject.toml

@@ -0,0 +1,70 @@
+[project]
+name = "sci-report-analyzer"
+version = "1.0.0"
+description = "Track researchers' publications across sources and rank their venues, with per-person folders, notes and reports"
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+requires-python = ">=3.13"
+dependencies = [
+    "alembic>=1.20.0",
+    "beautifulsoup4>=4.15.0",
+    "httpx>=0.28.1",
+    "lark>=1.3.1",
+    "latex2mathml>=3.81.1",
+    "lxml>=6.1.3",
+    "nicegui>=3.17.1",
+    "pydantic>=2.13.5",
+    "sqlalchemy>=2.1.1",
+]
+
+[[project.authors]]
+name = "Benjamin Piwowarski"
+email = "benjamin@piwowarski.fr"
+
+[project.scripts]
+sci-report-analyzer = "sci_report_analyzer.main:main"
+
+[build-system]
+requires = ["uv_build>=0.12.17,<0.13.0"]
+build-backend = "uv_build"
+
+[dependency-groups]
+dev = [
+    "pre-commit>=4.6.2",
+    "pytest>=9.1.1",
+    "pytest-asyncio>=1.4.0",
+    "respx>=0.23.1",
+    "ruff>=0.16.9",
+]
+
+[tool.ruff]
+line-length = 100
+target-version = "py313"
+
+[tool.ruff.lint]
+select = [
+    "E",
+    "F",
+    "W",
+    "I",
+    "UP",
+    "B",
+    "SIM",
+    "RUF",
+]
+ignore = [
+    "RUF001",
+    "RUF002",
+    "RUF003",
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/*" = ["E501"]
+"src/sci_report_analyzer/db/migrations/versions/*" = ["E501"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+asyncio_mode = "auto"
+markers = ["live: hits real remote APIs (run with -m live)"]
+addopts = "-m 'not live'"

sci_report_analyzer-1.0.0/pyproject.toml.orig

@@ -0,0 +1,56 @@
+[project]
+name = "sci-report-analyzer"
+version = "1.0.0"
+description = "Track researchers' publications across sources and rank their venues, with per-person folders, notes and reports"
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+authors = [
+    { name = "Benjamin Piwowarski", email = "benjamin@piwowarski.fr" }
+]
+requires-python = ">=3.13"
+dependencies = [
+    "alembic>=1.20.0",
+    "beautifulsoup4>=4.15.0",
+    "httpx>=0.28.1",
+    "lark>=1.3.1",
+    "latex2mathml>=3.81.1",
+    "lxml>=6.1.3",
+    "nicegui>=3.17.1",
+    "pydantic>=2.13.5",
+    "sqlalchemy>=2.1.1",
+]
+
+[project.scripts]
+sci-report-analyzer = "sci_report_analyzer.main:main"
+
+[build-system]
+requires = ["uv_build>=0.12.17,<0.13.0"]
+build-backend = "uv_build"
+
+[dependency-groups]
+dev = [
+    "pre-commit>=4.6.2",
+    "pytest>=9.1.1",
+    "pytest-asyncio>=1.4.0",
+    "respx>=0.23.1",
+    "ruff>=0.16.9",
+]
+
+[tool.ruff]
+line-length = 100
+target-version = "py313"
+
+[tool.ruff.lint]
+select = ["E", "F", "W", "I", "UP", "B", "SIM", "RUF"]
+ignore = ["RUF001", "RUF002", "RUF003"]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/*" = ["E501"]
+"src/sci_report_analyzer/db/migrations/versions/*" = ["E501"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+asyncio_mode = "auto"
+markers = ["live: hits real remote APIs (run with -m live)"]
+addopts = "-m 'not live'"

sci_report_analyzer-1.0.0/src/sci_report_analyzer/__init__.py

@@ -0,0 +1,6 @@
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("sci-report-analyzer")
+except PackageNotFoundError:  # running from the sources without installing
+    __version__ = "dev"