From 0e9b39a16604ddee7bd6a369ae3ad4ea25a100cc Mon Sep 17 00:00:00 2001 From: Matthew Evans Date: Wed, 22 Oct 2025 17:25:36 +0200 Subject: [PATCH 1/6] Fix mismatched package/module name --- {beam => datatractor_beam}/__init__.py | 0 pyproject.toml | 4 ++-- tests/test_mpr.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) rename {beam => datatractor_beam}/__init__.py (100%) diff --git a/beam/__init__.py b/datatractor_beam/__init__.py similarity index 100% rename from beam/__init__.py rename to datatractor_beam/__init__.py diff --git a/pyproject.toml b/pyproject.toml index 77342c1..ccbeef6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,7 @@ source = "vcs" version-file = "_version.py" [tool.hatch.build.targets.wheel] -packages = ["beam"] +packages = ["datatractor_beam"] [project] name = "datatractor-beam" @@ -57,7 +57,7 @@ dev = [ repository = "https://github.com/datatractor/beam" [project.scripts] -datatractor = "beam:run_datatractor" +datatractor = "datatractor_beam:run_datatractor" [tool.ruff] extend-exclude = [ diff --git a/tests/test_mpr.py b/tests/test_mpr.py index 150123a..ad086cc 100644 --- a/tests/test_mpr.py +++ b/tests/test_mpr.py @@ -4,7 +4,7 @@ import pytest -from beam import ExtractorPlan, SupportedExecutionMethod, extract +from datatractor_beam import ExtractorPlan, SupportedExecutionMethod, extract @pytest.fixture From 3e6341a13a2424d7d2e146398243090be293a103 Mon Sep 17 00:00:00 2001 From: Matthew Evans Date: Wed, 22 Oct 2025 17:26:05 +0200 Subject: [PATCH 2/6] Update publication in README --- README.md | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index aa02ebe..700ee55 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,14 @@ Repository containing the reference implementation of the Datatractor API, published at [![Datatractor Yard](https://badgen.net/static/%F0%9F%9A%9Cdatatractor/yard)](https://yard.datatractor.org/). -For more information, see the preprint: +For more information, see the publication: + +> **Datatractor: Metadata, automation, and registries for extractor interoperability in the chemical and materials sciences** +> Matthew L. Evans, Gian-Marco Rignanese, David Elbert & Peter Kraus +> MRS Bulletin, 50, 838-845 (2025) [DOI: 10.1557/s43577-025-00925-8](https://link.springer.com/article/10.1557/s43577-025-00925-8) + + +or preprint at: > **Datatractor: Metadata, automation, and registries for extractor interoperability in the chemical and materials sciences** > Matthew L. Evans, Gian-Marco Rignanese, David Elbert & Peter Kraus From be286e6d0d90f51bd051e9e802c6a2f553deaf3a Mon Sep 17 00:00:00 2001 From: Matthew Evans Date: Wed, 22 Oct 2025 17:41:27 +0200 Subject: [PATCH 3/6] Fix docs build --- docs/source/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 76d9499..6677cb1 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -13,7 +13,7 @@ import os import sys -sys.path.insert(0, os.path.abspath(os.path.join("..", "..", "beam"))) +sys.path.insert(0, os.path.abspath(os.path.join("..", "..", "datatractor_beam"))) version = "main" From 86c47e737d207d4a9a0114354de855e538dffd14 Mon Sep 17 00:00:00 2001 From: Peter Kraus Date: Wed, 22 Oct 2025 21:12:00 +0200 Subject: [PATCH 4/6] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 700ee55..a18756a 100644 --- a/README.md +++ b/README.md @@ -48,7 +48,7 @@ pip install . ### Usage #### As a Python module -To extract data from a file, you can use the `extract` function from the `beam` module inside your own Python code: +To extract data from a file, you can use the `extract` function from the `datatractor_beam` module inside your own Python code: ```python from datatractor_beam import extract From b55cf971454283e3549aab03b466285ba4f38928 Mon Sep 17 00:00:00 2001 From: Peter Kraus Date: Wed, 22 Oct 2025 21:17:01 +0200 Subject: [PATCH 5/6] more beams --- docs/source/index.rst | 2 +- scripts/biologic-mpr-example.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index 4583d21..e2f43f5 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -7,7 +7,7 @@ Datatractor Beam: Reference implementation of the Datatractor API :hidden: :glob: - apidoc/beam + apidoc/datatractor_beam Documentation of |beamrepo|_, the reference implementation of the Datatractor API, diff --git a/scripts/biologic-mpr-example.py b/scripts/biologic-mpr-example.py index 204802d..e255be0 100644 --- a/scripts/biologic-mpr-example.py +++ b/scripts/biologic-mpr-example.py @@ -1,7 +1,7 @@ import pathlib import urllib.request -from beam import extract +from datatractor_beam import extract # Download an example MPR file from the registry download_path = pathlib.Path(__file__).parent / "data" / "example.mpr" From fea284a14dffa4c36498d6e12b6115faba1441fb Mon Sep 17 00:00:00 2001 From: Peter Kraus Date: Wed, 22 Oct 2025 21:20:53 +0200 Subject: [PATCH 6/6] package names are tough --- .github/workflows/build-docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml index f980e6b..63e1968 100644 --- a/.github/workflows/build-docs.yml +++ b/.github/workflows/build-docs.yml @@ -26,7 +26,7 @@ jobs: - name: Build docs run: | - sphinx-apidoc -o docs/source/apidoc beam + sphinx-apidoc -o docs/source/apidoc datatractor_beam sphinx-build -b html docs/source/ public/main - name: Upload docs artifact