rxiv2pdf 0.1.0__tar.gz

rxiv2pdf-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Ali Zaeim
+
+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.

rxiv2pdf-0.1.0/PKG-INFO

@@ -0,0 +1,191 @@
+Metadata-Version: 2.4
+Name: rxiv2pdf
+Version: 0.1.0
+Summary: Turn a bioRxiv/medRxiv preprint into a two-column, journal-style PDF built from its JATS XML.
+Keywords: biorxiv,medrxiv,preprint,jats,pdf,typst
+Author: Ali Zaeim
+License-Expression: MIT AND OFL-1.1
+License-File: LICENSE
+License-File: src/rxiv2pdf/fonts/OFL-SourceSans3.md
+License-File: src/rxiv2pdf/fonts/OFL-SourceSerif4.md
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Text Processing :: Markup :: XML
+Requires-Dist: httpx>=0.27
+Requires-Dist: lxml>=5.3
+Requires-Dist: pillow>=11.0
+Requires-Dist: rich>=13.7
+Requires-Dist: typer>=0.16
+Requires-Dist: typst>=0.15
+Requires-Python: >=3.11
+Project-URL: Homepage, https://github.com/ali-zaeim/rxiv2pdf
+Project-URL: Repository, https://github.com/ali-zaeim/rxiv2pdf
+Project-URL: Issues, https://github.com/ali-zaeim/rxiv2pdf/issues
+Project-URL: Changelog, https://github.com/ali-zaeim/rxiv2pdf/blob/main/CHANGELOG.md
+Description-Content-Type: text/markdown
+
+# rxiv2pdf
+
+[![CI](https://github.com/ali-zaeim/rxiv2pdf/actions/workflows/ci.yml/badge.svg)](https://github.com/ali-zaeim/rxiv2pdf/actions/workflows/ci.yml)
+[![PyPI](https://img.shields.io/pypi/v/rxiv2pdf)](https://pypi.org/project/rxiv2pdf/)
+[![Python](https://img.shields.io/pypi/pyversions/rxiv2pdf)](https://pypi.org/project/rxiv2pdf/)
+[![License: MIT](https://img.shields.io/badge/license-MIT-blue)](https://github.com/ali-zaeim/rxiv2pdf/blob/main/LICENSE)
+
+Turn a bioRxiv or medRxiv preprint into a two-column, journal-style PDF.
+
+The PDF on bioRxiv and medRxiv is the authors' submitted manuscript, often double-spaced and
+line-numbered, with the figures at the end. rxiv2pdf rebuilds the paper from the preprint's JATS
+XML instead, with each figure placed after the text that first cites it and the citations linked
+to the references.
+
+```console
+$ rxiv2pdf https://www.biorxiv.org/content/10.64898/2026.10.16.759679v1
+PDF  2026.10.16.759679v1.pdf
+```
+
+| Page 1 | A figure page |
+|:--:|:--:|
+| ![Page 1: front matter, abstract box, two-column body](https://raw.githubusercontent.com/ali-zaeim/rxiv2pdf/main/docs/screenshots/page1.png) | ![A full-width figure with its caption](https://raw.githubusercontent.com/ali-zaeim/rxiv2pdf/main/docs/screenshots/figure-page.png) |
+
+<sub>Screenshots on this page: Ghosh *et al.*, "Astrocytic sEH–EET signaling regulates microglial
+lysosomal function and suppresses the STING–Type I interferon pathway in Alzheimer's disease",
+bioRxiv [10.64898/2026.10.16.759679](https://doi.org/10.64898/2026.10.16.759679), CC BY 4.0.</sub>
+
+## Install
+
+Requires Python 3.11+. Typst comes with the `typst` Python package and the fonts are bundled, so
+nothing else is needed.
+
+```console
+$ pipx install rxiv2pdf        # or: uv tool install rxiv2pdf
+$ rxiv2pdf --help
+```
+
+`pip install rxiv2pdf` works too. To try it without installing anything:
+`uvx rxiv2pdf 10.1101/2024.04.17.590000`.
+
+## Usage
+
+```console
+$ rxiv2pdf 10.1101/2024.04.17.590000                  # bare DOI (bioRxiv by default, medRxiv tried next)
+$ rxiv2pdf https://www.medrxiv.org/content/10.64898/2026.09.25.26364016v1.full
+$ rxiv2pdf https://doi.org/10.64898/2026.10.22.760766 -o papers/ --theme compact --paper a4
+$ rxiv2pdf 10.1101/2020.03.22.002386v2                # a specific version (default: latest)
+$ rxiv2pdf --list dois.txt -o papers/                 # batch: one URL/DOI per line, # comments ok
+```
+
+All options are listed under [Options](#options).
+
+## What you get
+
+- **Front matter:** title, authors and affiliations, abstract, and a banner with the DOI, date and
+  version. Page 1 notes that the preprint isn't peer reviewed and gives its license.
+- **Two columns** with aligned baselines and a balanced last page.
+- **Figures and tables** after their first citation, full width when wide, and sized by their
+  lettering, so a simple chart isn't blown up. Long tables and figures after the references get
+  pages of their own.
+- **Linked citations,** collapsed into ranges, and DOI links in the references.
+- **Equations, back matter** (funding, data availability…) and a banner on withdrawn preprints.
+
+## Themes
+
+Choose a look with `--theme`:
+
+- `default`: serif body, numbered sans headings in navy, a shaded abstract box.
+- `compact`: a dense letters-journal look, with smaller serif text on narrow margins, a serif title,
+  a bold abstract, capitalised headings and run-in subheadings. About 20% fewer pages.
+- `sans`: a modern open-access look, with a teal band, a large title, ragged-right sans text, ruled
+  headings and bracketed citations.
+
+One column per theme, each showing page 1, page 2 and a figure page of the same preprint:
+
+![The same preprint in the three themes: page 1, page 2 and a figure page](https://raw.githubusercontent.com/ali-zaeim/rxiv2pdf/main/docs/screenshots/themes.png)
+
+## Options
+
+| Option | Description |
+|---|---|
+| `-o, --outdir DIR` | Where the PDF goes. Default: the current directory. |
+| `--preprint-version N` | Preprint version; overrides a `vN` in the URL. Default: the `vN` in the URL, else the latest. |
+| `--server biorxiv\|medrxiv` | Override server detection. Default: detected from the URL; a bare DOI tries bioRxiv, then medRxiv. |
+| `--theme default\|compact\|sans` | Look of the PDF; see [Themes](#themes). Default: `default`. |
+| `--paper letter\|a4` | Paper size. Default: `letter` (US Letter). |
+| `--list FILE` | Batch mode. Keeps going after failures, prints a summary, exits 1 if any failed. |
+| `--supplements` | Also download the supplementary files, into `<name>-supplements/` next to the PDF. They are listed and linked in the PDF either way. |
+| `--append-supplements` | Append the supplementary PDFs and images to the end of the PDF, one bookmarked section per file (other files, such as spreadsheets, stay linked). |
+| `--fallback-pdf` | If no JATS XML exists yet (very new posts), save the server's original PDF. |
+| `--refresh` | Ignore the cache and download again. |
+| `--open` | Open the PDF when done. |
+| `-v`, `-vv` | `-v`: log each figure download, list every figure and table, and print a traceback on internal errors. `-vv`: also log every HTTP request. |
+| `--version` | Show the rxiv2pdf version and exit. |
+
+Exit codes: 0 success, 1 failure (not found, no XML yet, network, internal error), 2 bad input,
+130 interrupted (re-run to resume from the cache).
+
+### Cache and rate limits
+
+Downloads are cached under `~/.cache/rxiv2pdf/` (`%LOCALAPPDATA%\rxiv2pdf\Cache` on Windows;
+`$XDG_CACHE_HOME` and `RXIV2PDF_CACHE_DIR` are honoured), so re-runs make no network requests
+unless you pass `--refresh`.
+
+bioRxiv rate-limits heavily: after about ten requests it asks clients to wait for up to 4 minutes.
+rxiv2pdf waits and carries on, so a paper with many figures can take a few minutes the first time.
+An interrupted run resumes where it stopped. To add a contact address to the User-Agent, set
+`RXIV2PDF_CONTACT=you@example.org`.
+
+## Limitations
+
+- **The PDF can differ slightly from the one on bioRxiv.** It is rebuilt from bioRxiv's XML
+  conversion of the submission, not from the authors' PDF. Tables, equations and the lettering
+  inside figures come only as images, so they can't be searched or copied as text. The conversion
+  sometimes drops a space or garbles a character; rxiv2pdf repairs the cases it recognises and
+  prints a `fixed: …` line for each kind. Details such as word counts or ORCID IDs on the authors'
+  title page aren't in the XML. The running text otherwise matches closely. If you find a
+  difference in a preprint you care about, please
+  [open an issue](https://github.com/ali-zaeim/rxiv2pdf/issues).
+- **Some false citations stay linked.** bioRxiv's XML sometimes marks numbers in superscript as
+  citations, such as residue labels like D118<sup>3.49</sup> or powers of ten; rxiv2pdf unlinks
+  those. A superscript range such as a peptide fragment (NTS<sup>8–13</sup>) looks exactly like a
+  citation range, so it stays linked. In the `default` and `compact` themes it still reads as on
+  bioRxiv; in `sans`, which brackets citations, it shows as NTS [8–13].
+- **Equation images can differ in size,** because authors export them at different zoom levels.
+- **The page before end-of-article figures can be sparse.** Those figures start a new page, so
+  the last page of text may hold only a few lines.
+- **CJK characters** aren't covered by the bundled fonts.
+- **Only bioRxiv and medRxiv are supported.** ChemRxiv, for example, publishes only the authors'
+  PDFs, so there is no XML to rebuild a paper from.
+
+## Development
+
+The pipeline is resolve → fetch → parse → render → compile, one module per stage in
+`src/rxiv2pdf/`. All styling lives in `templates/journal.typ`; themes are parameter sets in
+`templates/themes/`.
+
+```console
+$ uv sync                               # Python env with dev dependencies
+$ uv run pytest                         # offline tests
+$ uv run ruff check src tests scripts   # lint (CI runs this too)
+$ uv run pytest -m network              # live test against bioRxiv (slow: rate limits)
+$ UPDATE_SNAPSHOTS=1 uv run pytest tests/test_jats.py   # after an intended model change
+$ uv run python scripts/preview.py previews/            # page-1 PNG of every fixture
+```
+
+`tests/fixtures/` holds real bioRxiv/medRxiv API responses and JATS XML, and `tests/snapshots/`
+the parsed model of each as JSON. bioRxiv supplies every table and equation as an image, so the
+XML-table and MathML code is tested on native-JATS articles from other journals in
+`tests/fixtures/external/` (sources and licenses in its README).
+
+## License
+
+rxiv2pdf is released under the MIT License (see `LICENSE`). Bundled fonts: Source Serif 4 and
+Source Sans 3 (SIL Open Font License 1.1, see `src/rxiv2pdf/fonts/`).
+
+rxiv2pdf is meant for personal reading. A rebuilt PDF is a derivative of the preprint, so sharing
+it must follow the preprint's own license, which is printed on page 1.

rxiv2pdf-0.1.0/README.md

@@ -0,0 +1,158 @@
+# rxiv2pdf
+
+[![CI](https://github.com/ali-zaeim/rxiv2pdf/actions/workflows/ci.yml/badge.svg)](https://github.com/ali-zaeim/rxiv2pdf/actions/workflows/ci.yml)
+[![PyPI](https://img.shields.io/pypi/v/rxiv2pdf)](https://pypi.org/project/rxiv2pdf/)
+[![Python](https://img.shields.io/pypi/pyversions/rxiv2pdf)](https://pypi.org/project/rxiv2pdf/)
+[![License: MIT](https://img.shields.io/badge/license-MIT-blue)](https://github.com/ali-zaeim/rxiv2pdf/blob/main/LICENSE)
+
+Turn a bioRxiv or medRxiv preprint into a two-column, journal-style PDF.
+
+The PDF on bioRxiv and medRxiv is the authors' submitted manuscript, often double-spaced and
+line-numbered, with the figures at the end. rxiv2pdf rebuilds the paper from the preprint's JATS
+XML instead, with each figure placed after the text that first cites it and the citations linked
+to the references.
+
+```console
+$ rxiv2pdf https://www.biorxiv.org/content/10.64898/2026.10.16.759679v1
+PDF  2026.10.16.759679v1.pdf
+```
+
+| Page 1 | A figure page |
+|:--:|:--:|
+| ![Page 1: front matter, abstract box, two-column body](https://raw.githubusercontent.com/ali-zaeim/rxiv2pdf/main/docs/screenshots/page1.png) | ![A full-width figure with its caption](https://raw.githubusercontent.com/ali-zaeim/rxiv2pdf/main/docs/screenshots/figure-page.png) |
+
+<sub>Screenshots on this page: Ghosh *et al.*, "Astrocytic sEH–EET signaling regulates microglial
+lysosomal function and suppresses the STING–Type I interferon pathway in Alzheimer's disease",
+bioRxiv [10.64898/2026.10.16.759679](https://doi.org/10.64898/2026.10.16.759679), CC BY 4.0.</sub>
+
+## Install
+
+Requires Python 3.11+. Typst comes with the `typst` Python package and the fonts are bundled, so
+nothing else is needed.
+
+```console
+$ pipx install rxiv2pdf        # or: uv tool install rxiv2pdf
+$ rxiv2pdf --help
+```
+
+`pip install rxiv2pdf` works too. To try it without installing anything:
+`uvx rxiv2pdf 10.1101/2024.04.17.590000`.
+
+## Usage
+
+```console
+$ rxiv2pdf 10.1101/2024.04.17.590000                  # bare DOI (bioRxiv by default, medRxiv tried next)
+$ rxiv2pdf https://www.medrxiv.org/content/10.64898/2026.09.25.26364016v1.full
+$ rxiv2pdf https://doi.org/10.64898/2026.10.22.760766 -o papers/ --theme compact --paper a4
+$ rxiv2pdf 10.1101/2020.03.22.002386v2                # a specific version (default: latest)
+$ rxiv2pdf --list dois.txt -o papers/                 # batch: one URL/DOI per line, # comments ok
+```
+
+All options are listed under [Options](#options).
+
+## What you get
+
+- **Front matter:** title, authors and affiliations, abstract, and a banner with the DOI, date and
+  version. Page 1 notes that the preprint isn't peer reviewed and gives its license.
+- **Two columns** with aligned baselines and a balanced last page.
+- **Figures and tables** after their first citation, full width when wide, and sized by their
+  lettering, so a simple chart isn't blown up. Long tables and figures after the references get
+  pages of their own.
+- **Linked citations,** collapsed into ranges, and DOI links in the references.
+- **Equations, back matter** (funding, data availability…) and a banner on withdrawn preprints.
+
+## Themes
+
+Choose a look with `--theme`:
+
+- `default`: serif body, numbered sans headings in navy, a shaded abstract box.
+- `compact`: a dense letters-journal look, with smaller serif text on narrow margins, a serif title,
+  a bold abstract, capitalised headings and run-in subheadings. About 20% fewer pages.
+- `sans`: a modern open-access look, with a teal band, a large title, ragged-right sans text, ruled
+  headings and bracketed citations.
+
+One column per theme, each showing page 1, page 2 and a figure page of the same preprint:
+
+![The same preprint in the three themes: page 1, page 2 and a figure page](https://raw.githubusercontent.com/ali-zaeim/rxiv2pdf/main/docs/screenshots/themes.png)
+
+## Options
+
+| Option | Description |
+|---|---|
+| `-o, --outdir DIR` | Where the PDF goes. Default: the current directory. |
+| `--preprint-version N` | Preprint version; overrides a `vN` in the URL. Default: the `vN` in the URL, else the latest. |
+| `--server biorxiv\|medrxiv` | Override server detection. Default: detected from the URL; a bare DOI tries bioRxiv, then medRxiv. |
+| `--theme default\|compact\|sans` | Look of the PDF; see [Themes](#themes). Default: `default`. |
+| `--paper letter\|a4` | Paper size. Default: `letter` (US Letter). |
+| `--list FILE` | Batch mode. Keeps going after failures, prints a summary, exits 1 if any failed. |
+| `--supplements` | Also download the supplementary files, into `<name>-supplements/` next to the PDF. They are listed and linked in the PDF either way. |
+| `--append-supplements` | Append the supplementary PDFs and images to the end of the PDF, one bookmarked section per file (other files, such as spreadsheets, stay linked). |
+| `--fallback-pdf` | If no JATS XML exists yet (very new posts), save the server's original PDF. |
+| `--refresh` | Ignore the cache and download again. |
+| `--open` | Open the PDF when done. |
+| `-v`, `-vv` | `-v`: log each figure download, list every figure and table, and print a traceback on internal errors. `-vv`: also log every HTTP request. |
+| `--version` | Show the rxiv2pdf version and exit. |
+
+Exit codes: 0 success, 1 failure (not found, no XML yet, network, internal error), 2 bad input,
+130 interrupted (re-run to resume from the cache).
+
+### Cache and rate limits
+
+Downloads are cached under `~/.cache/rxiv2pdf/` (`%LOCALAPPDATA%\rxiv2pdf\Cache` on Windows;
+`$XDG_CACHE_HOME` and `RXIV2PDF_CACHE_DIR` are honoured), so re-runs make no network requests
+unless you pass `--refresh`.
+
+bioRxiv rate-limits heavily: after about ten requests it asks clients to wait for up to 4 minutes.
+rxiv2pdf waits and carries on, so a paper with many figures can take a few minutes the first time.
+An interrupted run resumes where it stopped. To add a contact address to the User-Agent, set
+`RXIV2PDF_CONTACT=you@example.org`.
+
+## Limitations
+
+- **The PDF can differ slightly from the one on bioRxiv.** It is rebuilt from bioRxiv's XML
+  conversion of the submission, not from the authors' PDF. Tables, equations and the lettering
+  inside figures come only as images, so they can't be searched or copied as text. The conversion
+  sometimes drops a space or garbles a character; rxiv2pdf repairs the cases it recognises and
+  prints a `fixed: …` line for each kind. Details such as word counts or ORCID IDs on the authors'
+  title page aren't in the XML. The running text otherwise matches closely. If you find a
+  difference in a preprint you care about, please
+  [open an issue](https://github.com/ali-zaeim/rxiv2pdf/issues).
+- **Some false citations stay linked.** bioRxiv's XML sometimes marks numbers in superscript as
+  citations, such as residue labels like D118<sup>3.49</sup> or powers of ten; rxiv2pdf unlinks
+  those. A superscript range such as a peptide fragment (NTS<sup>8–13</sup>) looks exactly like a
+  citation range, so it stays linked. In the `default` and `compact` themes it still reads as on
+  bioRxiv; in `sans`, which brackets citations, it shows as NTS [8–13].
+- **Equation images can differ in size,** because authors export them at different zoom levels.
+- **The page before end-of-article figures can be sparse.** Those figures start a new page, so
+  the last page of text may hold only a few lines.
+- **CJK characters** aren't covered by the bundled fonts.
+- **Only bioRxiv and medRxiv are supported.** ChemRxiv, for example, publishes only the authors'
+  PDFs, so there is no XML to rebuild a paper from.
+
+## Development
+
+The pipeline is resolve → fetch → parse → render → compile, one module per stage in
+`src/rxiv2pdf/`. All styling lives in `templates/journal.typ`; themes are parameter sets in
+`templates/themes/`.
+
+```console
+$ uv sync                               # Python env with dev dependencies
+$ uv run pytest                         # offline tests
+$ uv run ruff check src tests scripts   # lint (CI runs this too)
+$ uv run pytest -m network              # live test against bioRxiv (slow: rate limits)
+$ UPDATE_SNAPSHOTS=1 uv run pytest tests/test_jats.py   # after an intended model change
+$ uv run python scripts/preview.py previews/            # page-1 PNG of every fixture
+```
+
+`tests/fixtures/` holds real bioRxiv/medRxiv API responses and JATS XML, and `tests/snapshots/`
+the parsed model of each as JSON. bioRxiv supplies every table and equation as an image, so the
+XML-table and MathML code is tested on native-JATS articles from other journals in
+`tests/fixtures/external/` (sources and licenses in its README).
+
+## License
+
+rxiv2pdf is released under the MIT License (see `LICENSE`). Bundled fonts: Source Serif 4 and
+Source Sans 3 (SIL Open Font License 1.1, see `src/rxiv2pdf/fonts/`).
+
+rxiv2pdf is meant for personal reading. A rebuilt PDF is a derivative of the preprint, so sharing
+it must follow the preprint's own license, which is printed on page 1.

rxiv2pdf-0.1.0/pyproject.toml

@@ -0,0 +1,66 @@
+[project]
+name = "rxiv2pdf"
+version = "0.1.0"
+description = "Turn a bioRxiv/medRxiv preprint into a two-column, journal-style PDF built from its JATS XML."
+readme = "README.md"
+license = "MIT AND OFL-1.1"
+license-files = [
+    "LICENSE",
+    "src/rxiv2pdf/fonts/OFL-*.md",
+]
+requires-python = ">=3.11"
+keywords = [
+    "biorxiv",
+    "medrxiv",
+    "preprint",
+    "jats",
+    "pdf",
+    "typst",
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Text Processing :: Markup :: XML",
+]
+dependencies = [
+    "httpx>=0.27",
+    "lxml>=5.3",
+    "pillow>=11.0",
+    "rich>=13.7",
+    "typer>=0.16",
+    "typst>=0.15",
+]
+
+[[project.authors]]
+name = "Ali Zaeim"
+
+[project.scripts]
+rxiv2pdf = "rxiv2pdf.cli:main"
+
+[project.urls]
+Homepage = "https://github.com/ali-zaeim/rxiv2pdf"
+Repository = "https://github.com/ali-zaeim/rxiv2pdf"
+Issues = "https://github.com/ali-zaeim/rxiv2pdf/issues"
+Changelog = "https://github.com/ali-zaeim/rxiv2pdf/blob/main/CHANGELOG.md"
+
+[dependency-groups]
+dev = [
+    "pytest>=8.3",
+    "ruff>=0.17,<0.18",
+]
+
+[build-system]
+requires = ["uv_build>=0.8,<0.14"]
+build-backend = "uv_build"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-m 'not network'"
+markers = ["network: hits the live bioRxiv/medRxiv servers (run with: pytest -m network)"]

rxiv2pdf-0.1.0/pyproject.toml.orig

@@ -0,0 +1,53 @@
+[project]
+name = "rxiv2pdf"
+version = "0.1.0"
+description = "Turn a bioRxiv/medRxiv preprint into a two-column, journal-style PDF built from its JATS XML."
+readme = "README.md"
+license = "MIT AND OFL-1.1"  # code MIT; bundled Source Serif/Sans fonts OFL-1.1
+license-files = ["LICENSE", "src/rxiv2pdf/fonts/OFL-*.md"]
+authors = [{ name = "Ali Zaeim" }]
+requires-python = ">=3.11"
+keywords = ["biorxiv", "medrxiv", "preprint", "jats", "pdf", "typst"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Text Processing :: Markup :: XML",
+]
+dependencies = [
+    "httpx>=0.27",
+    "lxml>=5.3",
+    "pillow>=11.0",
+    "rich>=13.7",
+    "typer>=0.16",  # older versions crash on --help with Click 8.2+
+    "typst>=0.15",  # Compiler.compile_with_warnings / query with sys_inputs
+]
+
+[project.scripts]
+rxiv2pdf = "rxiv2pdf.cli:main"
+
+[project.urls]
+Homepage = "https://github.com/ali-zaeim/rxiv2pdf"
+Repository = "https://github.com/ali-zaeim/rxiv2pdf"
+Issues = "https://github.com/ali-zaeim/rxiv2pdf/issues"
+Changelog = "https://github.com/ali-zaeim/rxiv2pdf/blob/main/CHANGELOG.md"
+
+[dependency-groups]
+dev = ["pytest>=8.3", "ruff>=0.17,<0.18"]  # ruff pinned: its default rule set changes between minor versions
+
+[build-system]
+requires = ["uv_build>=0.8,<0.14"]
+build-backend = "uv_build"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-m 'not network'"
+markers = [
+    "network: hits the live bioRxiv/medRxiv servers (run with: pytest -m network)",
+]

rxiv2pdf-0.1.0/src/rxiv2pdf/__init__.py

@@ -0,0 +1,8 @@
+"""rxiv2pdf: bioRxiv/medRxiv preprint -> journal-style PDF, built from JATS XML."""
+
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("rxiv2pdf")  # single source: pyproject.toml
+except PackageNotFoundError:  # running from a source tree that was never installed
+    __version__ = "0.0.0+unknown"

rxiv2pdf-0.1.0/src/rxiv2pdf/__main__.py

@@ -0,0 +1,5 @@
+"""`python -m rxiv2pdf` runs the CLI."""
+
+from .cli import main
+
+main()