diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index ae1d308..f2d0dbd 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -24,7 +24,7 @@ defaults: jobs: main-tests: - if: "github.repository == 'yoshanuikabundi/openff-pablo'" + if: "github.repository == 'openforcefield/openff-pablo'" runs-on: ${{ matrix.os }} strategy: fail-fast: false diff --git a/AUTHORS.md b/AUTHORS.md index 535f7b4..bac39f0 100644 --- a/AUTHORS.md +++ b/AUTHORS.md @@ -4,7 +4,7 @@ OpenFF Pablo was created by Josh Mitchell in 2025. All contributing authors are listed in this file below. -The repository history at https://github.com/yoshanuikabundi/openff-pablo +The repository history at https://github.com/openforcefield/openff-pablo and the CHANGELOG show individual code contributions. ## Chronological list of authors diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index b40152e..c0b1236 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -4,12 +4,12 @@ We welcome all contributions to OpenFF Pablo! Contributions can take many forms, such as: -* sharing bug reports or feature requests through the [Issue Tracker](https://github.com/yoshanuikabundi/openff-pablo/issues) +* sharing bug reports or feature requests through the [Issue Tracker](https://github.com/openforcefield/openff-pablo/issues) * asking or answering questions, or otherwise joining in on discussions * adding bug fixes, new features, or otherwise improving the code * adding or improving documentation -The second two options both involve making a [pull request](https://github.com/yoshanuikabundi/openff-pablo/pulls) . +The second two options both involve making a [pull request](https://github.com/openforcefield/openff-pablo/pulls) . There are many existing guides on how to make a contribution to an open source project on GitHub. In short, the steps are to: diff --git a/README.md b/README.md index 4cac349..8eb825a 100644 --- a/README.md +++ b/README.md @@ -2,13 +2,13 @@ OpenFF Pablo ============================== [//]: # (Badges) -| **Latest release** | [![Last release tag](https://img.shields.io/github/release-pre/yoshanuikabundi/openff-pablo.svg)](https://github.com/openforcefield/openff-pablo/releases) ![GitHub commits since latest release (by date) for a branch](https://img.shields.io/github/commits-since/openforcefield/openff-pablo/latest) [![Documentation Status](https://readthedocs.org/projects/openff-pablo/badge/?version=latest)](https://openff-pablo.readthedocs.io/en/latest/?badge=latest) | +| **Latest release** | [![Last release tag](https://img.shields.io/github/release-pre/openforcefield/openff-pablo.svg)](https://github.com/openforcefield/openff-pablo/releases) ![GitHub commits since latest release (by date) for a branch](https://img.shields.io/github/commits-since/openforcefield/openff-pablo/latest) [![Documentation Status](https://readthedocs.org/projects/openff-pablo/badge/?version=latest)](https://openff-pablo.readthedocs.io/en/latest/?badge=latest) | | :----------------- | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| **Status** | [![GH Actions Status](https://github.com/yoshanuikabundi/openff-pablo/actions/workflows/gh-ci.yaml/badge.svg)](https://github.com/openforcefield/openff-pablo/actions?query=branch%3Amain+workflow%3Agh-ci) | +| **Status** | [![GH Actions Status](https://github.com/openforcefield/openff-pablo/actions/workflows/gh-ci.yaml/badge.svg)](https://github.com/openforcefield/openff-pablo/actions?query=branch%3Amain+workflow%3Agh-ci) | New, independent implementation of `Topology.from_pdb` -OpenFF Pablo is bound by a [Code of Conduct](https://github.com/yoshanuikabundi/openff-pablo/blob/main/CODE_OF_CONDUCT.md). +OpenFF Pablo is bound by a [Code of Conduct](https://github.com/openforcefield/openff-pablo/blob/main/CODE_OF_CONDUCT.md). ### Installation @@ -72,8 +72,8 @@ pip install -e ".[test,doc]" ### Copyright -The OpenFF Pablo source code is hosted at https://github.com/yoshanuikabundi/openff-pablo -and is available under the GNU General Public License, version 3 (see the file [LICENSE](https://github.com/yoshanuikabundi/openff-pablo/blob/main/LICENSE)). +The OpenFF Pablo source code is hosted at https://github.com/openforcefield/openff-pablo +and is available under the GNU General Public License, version 3 (see the file [LICENSE](https://github.com/openforcefield/openff-pablo/blob/main/LICENSE)). Copyright (c) 2025, Josh Mitchell diff --git a/docs/conf.py b/docs/conf.py index b4436e9..c50c62c 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -241,7 +241,7 @@ html_theme_options = { # Repository integration # Set the repo url for the link to appear - "repo_url": "https://github.com/yoshanuikabundi/openff-pablo", + "repo_url": "https://github.com/openforcefield/openff-pablo", # The name of the repo. If must be set if repo_url is set "repo_name": "openff-pablo", # Must be one of github, gitlab or bitbucket diff --git a/docs/tests.md b/docs/tests.md index d69b2d0..7a5bdd8 100644 --- a/docs/tests.md +++ b/docs/tests.md @@ -13,6 +13,8 @@ Pablo has a (developing) PDB test suite. - Coverage * - 5ap1_prepared.pdb - ACE/NME caps, `unique_molecules` +* - 193L_prepared.pdb + - disulfides, all 20 canonical amino acids, charged terminii, charged canonical AA side chains :::