paperpush 0.1.0__tar.gz

paperpush-0.1.0/LICENSE

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+BSD 2-Clause License
+
+Copyright (c) 2024, Pachter Lab
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

paperpush-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: paperpush
+Version: 0.1.0
+Summary: A Python library for automating the submission of manuscripts to academic venues.
+Author-email: Joseph Rich <josephrich98@gmail.com>
+Maintainer-email: Joseph Rich <josephrich98@gmail.com>
+License: MIT
+Project-URL: Homepage, https://github.com/pachterlab/paperpush
+Project-URL: Repository, https://github.com/pachterlab/paperpush
+Project-URL: Documentation, https://github.com/pachterlab/paperpush#readme
+Project-URL: Issues, https://github.com/pachterlab/paperpush/issues
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: playwright>=1.40
+Requires-Dist: keyring>=24.0
+Requires-Dist: pydantic>=2.0
+Requires-Dist: pypdf>=6.0.0
+Requires-Dist: pillow>=10.0
+Provides-Extra: autofill
+Requires-Dist: anthropic>=0.40; extra == "autofill"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: bandit; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: chromium; extra == "dev"
+Requires-Dist: jsonschema>=4.18; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: isort; extra == "dev"
+Dynamic: license-file
+
+# PaperPush: Automated manuscript submission to journals, conferences, and preprint servers
+
+<!-- [![Documentation Status](https://readthedocs.org/projects/paperpush/badge/?version=latest)](https://paperpush.readthedocs.io/en/latest/?badge=latest) -->
+
+Prepare manuscripts for submission to preprint servers, venues, and conferences with just a few commands. No need to spend hours filling out forms manually. Just provide a manuscript directory and submission venue of interest, and `paperpush` will fill out the submission portal for you.
+
+## Install
+
+```bash
+pip install paperpush
+```
+
+To install the playwright dependency and the required browsers, run:
+
+```bash
+playwright install
+```
+
+## Use with AI
+```LLM
+Prepare my manuscript in /PATH/TO/MANUSCRIPT/DIRECTORY for submission to VENUE with PaperPush.
+```
+
+The Claude skill `/paperpush-prepare-submission` helps with this. 
+
+See [`docs/example-session.md`](docs/example-session.md) for a full worked example of this flow.
+
+## Quickstart
+1. `paperpush subfile VENUE`: creates a file VENUE.sub that is a template for the VENUE submission.
+2. **fill out VENUE.sub - 3 options:**
+   - **a.** *fill out manually*
+   - **b.** *Ask an LLM*: Use Claude skill `/paperpush-autofill`, or any AI agent following [`AGENTS.md`](AGENTS.md).
+   - **c.** `paperpush autofill -d /PATH/TO/MANUSCRIPT/DIRECTORY --engine api VENUE.sub`: Use an LLM API. Requires an API key.
+3. `paperpush validate VENUE.sub`: run the pre-submission checks on the filled `VENUE.sub`.
+4. `paperpush login VENUE`: log in to the VENUE submission portal
+5. `paperpush submit VENUE.sub`: Fill out the VENUE submission portal. Will not actually submit the manuscript. We highly recommend reviewing the submission form in the venue portal before clicking submit.
+
+## Run the whole pipeline at once
+
+`scripts/paperpush_pipeline.py` sequentially runs the commands above — `subfile`, `autofill`, `validate`, `login`, `submit`. This allows going from a manuscript directory to a filled submission portal in just one command.
+
+```bash
+python scripts/paperpush_pipeline.py -d /PATH/TO/MANUSCRIPT/DIRECTORY --engine api VENUE
+```
+
+See `python scripts/paperpush_pipeline.py --help` for the full list of options, grouped by step.
+
+## Supported venues
+
+<!-- BEGIN SUPPORTED VENUES -->
+**Preprint servers:** [arXiv](https://arxiv.org), [bioRxiv](https://www.biorxiv.org), [medRxiv](https://www.medrxiv.org)
+
+**Journals:** [Bioinformatics](https://academic.oup.com/bioinformatics), [BMC Bioinformatics](https://link.springer.com/journal/12859), [Cell](https://www.cell.com/cell/home), [Cell Genomics](https://www.cell.com/cell-genomics/home), [Cell Systems](https://www.cell.com/cell-systems/home), [Discrete Mathematics](https://www.sciencedirect.com/journal/discrete-mathematics), [Genome Biology](https://genomebiology.biomedcentral.com), [Nature](https://www.nature.com), [Nature Biotechnology](https://www.nature.com/nbt), [Nature Methods](https://www.nature.com/nmeth), [Nucleic Acids Research](https://academic.oup.com/nar), [PLOS Computational Biology](https://journal.plos.org/ploscompbiol/), [Science](https://www.science.org/journal/science), [Science Advances](https://www.science.org/journal/sciadv), [Science Immunology](https://www.science.org/journal/sciimmunol), [Science Robotics](https://www.science.org/journal/scirobotics), [Science Signaling](https://www.science.org/journal/signaling), [Science Translational Medicine](https://www.science.org/journal/stm)
+
+**Conferences:** _none yet_
+<!-- END SUPPORTED VENUES -->
+
+View the list on the command line with `paperpush --venues`.
+
+For more details, see [`venues.md`](venues.md)
+
+## Documentation
+
+[paperpush.readthedocs.io](https://paperpush.readthedocs.io)
+
+## Adding new venues
+
+See [`CONTRIBUTING.md`](CONTRIBUTING.md) for instructions on adding new venues. See [`DEVELOPMENT.md`](DEVELOPMENT.md) for tips on adding new venues and running unit tests.
+
+## For AI agents
+
+If you are an AI agent asked to submit a manuscript on the user's behalf, read
+[`AGENTS.md`](AGENTS.md). It describes how to run the full pipeline while doing
+your **own** field extraction (reading the manuscript and writing a
+`values.json` for the default `--engine manual`) rather than relying on the
+API-backed engine. Claude Code should prefer the `/paperpush-prepare-submission`
+and `/paperpush-autofill` skills, which encode the same contract.
+
+## License
+This project is licensed under the BSD-2 License - see the [LICENSE](LICENSE) file for details.
+
+Developed by Joe Rich

paperpush-0.1.0/README.md

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+# PaperPush: Automated manuscript submission to journals, conferences, and preprint servers
+
+<!-- [![Documentation Status](https://readthedocs.org/projects/paperpush/badge/?version=latest)](https://paperpush.readthedocs.io/en/latest/?badge=latest) -->
+
+Prepare manuscripts for submission to preprint servers, venues, and conferences with just a few commands. No need to spend hours filling out forms manually. Just provide a manuscript directory and submission venue of interest, and `paperpush` will fill out the submission portal for you.
+
+## Install
+
+```bash
+pip install paperpush
+```
+
+To install the playwright dependency and the required browsers, run:
+
+```bash
+playwright install
+```
+
+## Use with AI
+```LLM
+Prepare my manuscript in /PATH/TO/MANUSCRIPT/DIRECTORY for submission to VENUE with PaperPush.
+```
+
+The Claude skill `/paperpush-prepare-submission` helps with this. 
+
+See [`docs/example-session.md`](docs/example-session.md) for a full worked example of this flow.
+
+## Quickstart
+1. `paperpush subfile VENUE`: creates a file VENUE.sub that is a template for the VENUE submission.
+2. **fill out VENUE.sub - 3 options:**
+   - **a.** *fill out manually*
+   - **b.** *Ask an LLM*: Use Claude skill `/paperpush-autofill`, or any AI agent following [`AGENTS.md`](AGENTS.md).
+   - **c.** `paperpush autofill -d /PATH/TO/MANUSCRIPT/DIRECTORY --engine api VENUE.sub`: Use an LLM API. Requires an API key.
+3. `paperpush validate VENUE.sub`: run the pre-submission checks on the filled `VENUE.sub`.
+4. `paperpush login VENUE`: log in to the VENUE submission portal
+5. `paperpush submit VENUE.sub`: Fill out the VENUE submission portal. Will not actually submit the manuscript. We highly recommend reviewing the submission form in the venue portal before clicking submit.
+
+## Run the whole pipeline at once
+
+`scripts/paperpush_pipeline.py` sequentially runs the commands above — `subfile`, `autofill`, `validate`, `login`, `submit`. This allows going from a manuscript directory to a filled submission portal in just one command.
+
+```bash
+python scripts/paperpush_pipeline.py -d /PATH/TO/MANUSCRIPT/DIRECTORY --engine api VENUE
+```
+
+See `python scripts/paperpush_pipeline.py --help` for the full list of options, grouped by step.
+
+## Supported venues
+
+<!-- BEGIN SUPPORTED VENUES -->
+**Preprint servers:** [arXiv](https://arxiv.org), [bioRxiv](https://www.biorxiv.org), [medRxiv](https://www.medrxiv.org)
+
+**Journals:** [Bioinformatics](https://academic.oup.com/bioinformatics), [BMC Bioinformatics](https://link.springer.com/journal/12859), [Cell](https://www.cell.com/cell/home), [Cell Genomics](https://www.cell.com/cell-genomics/home), [Cell Systems](https://www.cell.com/cell-systems/home), [Discrete Mathematics](https://www.sciencedirect.com/journal/discrete-mathematics), [Genome Biology](https://genomebiology.biomedcentral.com), [Nature](https://www.nature.com), [Nature Biotechnology](https://www.nature.com/nbt), [Nature Methods](https://www.nature.com/nmeth), [Nucleic Acids Research](https://academic.oup.com/nar), [PLOS Computational Biology](https://journal.plos.org/ploscompbiol/), [Science](https://www.science.org/journal/science), [Science Advances](https://www.science.org/journal/sciadv), [Science Immunology](https://www.science.org/journal/sciimmunol), [Science Robotics](https://www.science.org/journal/scirobotics), [Science Signaling](https://www.science.org/journal/signaling), [Science Translational Medicine](https://www.science.org/journal/stm)
+
+**Conferences:** _none yet_
+<!-- END SUPPORTED VENUES -->
+
+View the list on the command line with `paperpush --venues`.
+
+For more details, see [`venues.md`](venues.md)
+
+## Documentation
+
+[paperpush.readthedocs.io](https://paperpush.readthedocs.io)
+
+## Adding new venues
+
+See [`CONTRIBUTING.md`](CONTRIBUTING.md) for instructions on adding new venues. See [`DEVELOPMENT.md`](DEVELOPMENT.md) for tips on adding new venues and running unit tests.
+
+## For AI agents
+
+If you are an AI agent asked to submit a manuscript on the user's behalf, read
+[`AGENTS.md`](AGENTS.md). It describes how to run the full pipeline while doing
+your **own** field extraction (reading the manuscript and writing a
+`values.json` for the default `--engine manual`) rather than relying on the
+API-backed engine. Claude Code should prefer the `/paperpush-prepare-submission`
+and `/paperpush-autofill` skills, which encode the same contract.
+
+## License
+This project is licensed under the BSD-2 License - see the [LICENSE](LICENSE) file for details.
+
+Developed by Joe Rich

paperpush-0.1.0/paperpush/__init__.py

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+"""paperpush: one-click manuscript submission to academic venues."""
+
+import logging
+
+__version__ = "0.1.0"
+__url__ = "https://github.com/pachterlab/paperpush"
+
+# Standard-library convention: a library should not configure logging output.
+# The NullHandler keeps importing paperpush silent until the embedding
+# application (or our own CLI, via paperpush._logging.configure_logging)
+# installs a real handler.
+#
+# Import stdlib logging under its own name -- NOT ``as _logging`` -- so it does
+# not shadow the ``paperpush._logging`` submodule as a package attribute, which
+# would make ``from paperpush import _logging`` hand back the stdlib module.
+logging.getLogger(__name__).addHandler(logging.NullHandler())
+
+# Public API. Kept deliberately small: the two data models (with their
+# accessors), the subfile toolkit, and the two workflow operations that have a
+# library-level entry point. The login and submit steps are exposed only as CLI
+# commands (`paperpush login` / `paperpush submit`), not as importable
+# functions. Lower-level helpers (autofill extraction internals, credential
+# storage, logging setup) remain importable from their submodules
+# (e.g. `from paperpush import credentials`) but are not part of the public API.
+from .database import Field, Venue, get_venue, list_venues
+from .subfile import SubFile, load, parse, render_template, write_template
+from .autofill import autofill
+from .validate import validate
+
+__all__ = [
+    "__version__",
+    "__url__",
+    # Data models
+    "Field",
+    "Venue",
+    "get_venue",
+    "list_venues",
+    # Submission files
+    "SubFile",
+    "load",
+    "parse",
+    "render_template",
+    "write_template",
+    # Workflow operations
+    "autofill",
+    "validate",
+]

paperpush-0.1.0/paperpush/_logging.py

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+"""Logging configuration for the paperpush command-line interface.
+
+Library modules obtain a logger with ``logging.getLogger(__name__)`` and never
+install handlers themselves. Following the standard-library convention, the
+package's top-level logger carries a :class:`logging.NullHandler` (attached in
+:mod:`paperpush.__init__`), so importing paperpush as a library stays
+silent unless the embedding application configures logging.
+
+The command-line entry point calls :func:`configure_logging` once to attach a
+single stderr handler whose level reflects the ``-v``/``-q`` flags, or the
+``PAPERPUSH_LOG_LEVEL`` environment variable when set. Diagnostics go to
+stderr so they never mix with command output on stdout.
+"""
+
+from __future__ import annotations
+
+import logging
+import os
+import sys
+
+PACKAGE_LOGGER = "paperpush"
+
+# Each additional ``-v`` raises the verbosity one step from the WARNING default:
+# -v -> INFO, -vv -> DEBUG.
+_VERBOSITY_LEVELS = [logging.WARNING, logging.INFO, logging.DEBUG]
+
+_LOG_FORMAT = "%(asctime)s %(levelname)s %(name)s: %(message)s"
+_DATE_FORMAT = "%H:%M:%S"
+
+# Marks the handler this module installs so a later call can replace it rather
+# than stack a second one.
+_HANDLER_FLAG = "_paperpush_cli_handler"
+
+
+def _level_from_env() -> int | None:
+    """Return the level named by ``PAPERPUSH_LOG_LEVEL``, or None if unset/bad."""
+    name = os.environ.get("PAPERPUSH_LOG_LEVEL")
+    if not name:
+        return None
+    resolved = logging.getLevelName(name.strip().upper())
+    # getLevelName returns the int for a known name, or a "Level X" string for
+    # an unknown one; only accept a real level.
+    return resolved if isinstance(resolved, int) else None
+
+
+def resolve_level(verbosity: int = 0, quiet: bool = False) -> int:
+    """Pick a logging level from the CLI flags and the environment.
+
+    ``PAPERPUSH_LOG_LEVEL`` (e.g. ``DEBUG``) wins when set to a valid level;
+    otherwise ``quiet`` forces ``ERROR`` and each ``-v`` raises the verbosity one
+    step from the ``WARNING`` default.
+    """
+    env_level = _level_from_env()
+    if env_level is not None:
+        return env_level
+    if quiet:
+        return logging.ERROR
+    index = min(max(verbosity, 0), len(_VERBOSITY_LEVELS) - 1)
+    return _VERBOSITY_LEVELS[index]
+
+
+def configure_logging(verbosity: int = 0, quiet: bool = False) -> logging.Logger:
+    """Attach a single stderr handler to the package logger and set its level.
+
+    Safe to call more than once: a handler installed by an earlier call is
+    replaced rather than stacked, so repeated CLI invocations within one process
+    (notably the test suite) do not emit duplicate lines.
+    """
+    level = resolve_level(verbosity, quiet)
+    logger = logging.getLogger(PACKAGE_LOGGER)
+
+    for handler in list(logger.handlers):
+        if getattr(handler, _HANDLER_FLAG, False):
+            logger.removeHandler(handler)
+
+    handler = logging.StreamHandler(sys.stderr)
+    handler.setFormatter(logging.Formatter(_LOG_FORMAT, _DATE_FORMAT))
+    setattr(handler, _HANDLER_FLAG, True)
+    logger.addHandler(handler)
+    logger.setLevel(level)
+    # Diagnostics flow only through our handler, not whatever the root logger has.
+    logger.propagate = False
+    logger.debug("Logging configured at level %s", logging.getLevelName(level))
+    return logger