From b74f9f6a28bbc657e05c05e5168dd11d29742b4c Mon Sep 17 00:00:00 2001 From: marjanalbouye Date: Thu, 19 Oct 2023 12:51:27 -0600 Subject: [PATCH 1/6] add missing DOIs --- paper/paper.bib | 25 +++++++++++-------------- 1 file changed, 11 insertions(+), 14 deletions(-) diff --git a/paper/paper.bib b/paper/paper.bib index 0b6c435b..83eddf3c 100644 --- a/paper/paper.bib +++ b/paper/paper.bib @@ -80,19 +80,15 @@ @article{chodera_2007 langid = {english}, } -@misc{hoomd_2019, - title = {{HOOMD}-blue: A Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations}, - url = {http://arxiv.org/abs/1308.5587}, - shorttitle = {{HOOMD}-blue}, - number = {{arXiv}:1308.5587}, - publisher = {{arXiv}}, - author = {Anderson, Joshua A. and Glaser, Jens and Glotzer, Sharon C.}, - urldate = {2023-10-03}, - date = {2019-10-18}, - langid = {english}, - eprinttype = {arxiv}, - eprint = {1308.5587 [physics]}, - keywords = {Physics - Computational Physics}, +@article{anderson2020hoomd, + title={HOOMD-blue: A Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations}, + author={Anderson, Joshua A and Glaser, Jens and Glotzer, Sharon C}, + journal={Computational Materials Science}, + volume={173}, + pages={109363}, + year={2020}, + publisher={Elsevier}, + doi={10.1016/j.commatsci.2019.109363} } @article{polyply_2022, @@ -144,7 +140,8 @@ @article{martin2018pyprism number={8}, pages={2906--2922}, year={2018}, - publisher={ACS Publications} + publisher={ACS Publications}, + doi={10.1021/acs.macromol.8b00011} } @Inbook{Klein2016mBuild, From accc73de1355733c44dbfc03b8276ea30603ed36 Mon Sep 17 00:00:00 2001 From: marjanalbouye Date: Thu, 19 Oct 2023 12:52:02 -0600 Subject: [PATCH 2/6] update country name --- paper/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/paper/paper.md b/paper/paper.md index 7c81751d..85abc4a7 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -24,7 +24,7 @@ authors: corresponding: true affiliation: 1 affiliations: - - name: Boise State University, Boise, ID, USA + - name: Boise State University, Boise, ID, United States of America index: 1 date: 16 October 2023 bibliography: paper.bib From 03b639d4caabb96237f75eded861e8feaa0770a0 Mon Sep 17 00:00:00 2001 From: marjanalbouye Date: Thu, 19 Oct 2023 13:16:04 -0600 Subject: [PATCH 3/6] make contributing guideline --- CONTRIBUTING.md | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 CONTRIBUTING.md diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 00000000..9f1eb036 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,36 @@ +# Contributing to flowerMD + +Thank you for considering contributing to flowerMD! We welcome all contributions +in the form of bug reports, feature requests, code contributions, suggestions, etc. + +The default branch for this repository is `main`. Please submit all pull requests +to the `main` branch. + +## Bug reports and feature requests +For bug reports and feature requests, please open an issue on the +[GitHub issue tracker](https://github.com/cmelab/flowerMD/issues). + +If you are reporting a bug, please include the following information: +- A short description of the bug +- A minimal working example that reproduces the bug +- The expected behavior +- The actual behavior +- The version of flowerMD you are using + +For feature requests, please include a short description of the feature you would +like to see added to flowerMD. + +## Code contributions +We welcome all code contributions in the form of pull requests. If you are +interested in contributing code, please follow the steps below: +- Fork the repository (default branch is `main`) +- Create a new branch for your feature/bug fix +- Create the `flowermd` conda environment using the `environment-cpu.yml` or `environment-gpu.yml` file +- Make your changes +- Install the latest version of pre-commit using `conda install -c conda-forge pre-commit` and run `pre-commit install` in the root directory of the repository +- Commit your changes and make sure all the pre-commit hooks pass +- Push your changes to your fork and create a pull request +- Assign the pull request to a reviewer and wait for the reviewers feedback + +New functionalities should be covered by unit tests. If you are adding a new +function/feature/class please follow the existing style for docstrings. \ No newline at end of file From 219bec1470a9d3509e6c16b9a6cda87c51b423e0 Mon Sep 17 00:00:00 2001 From: marjanalbouye Date: Thu, 19 Oct 2023 13:35:32 -0600 Subject: [PATCH 4/6] add contributing section --- README.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/README.md b/README.md index 371fd6da..d2cff320 100644 --- a/README.md +++ b/README.md @@ -39,6 +39,12 @@ how to use flowerMD and what functionalities it provides. ## Documentation Documentation is available at [https://flowermd.readthedocs.io](https://flowermd.readthedocs.io) +## Contributing +We welcome all contributions to flowerMD. Please see +[contributing guidelines](CONTRIBUTING.md) for more information. + + + [//]: # (#### Using the built in molecules, systems and forcefields:) [//]: # (README, documentation and tutorials are a work in progress.) From 14ff761d9d06fb0c641195ceb06bfac2ba161a43 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 19 Oct 2023 19:38:40 +0000 Subject: [PATCH 5/6] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- CONTRIBUTING.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 9f1eb036..bb699e1b 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,14 +1,14 @@ # Contributing to flowerMD -Thank you for considering contributing to flowerMD! We welcome all contributions +Thank you for considering contributing to flowerMD! We welcome all contributions in the form of bug reports, feature requests, code contributions, suggestions, etc. -The default branch for this repository is `main`. Please submit all pull requests +The default branch for this repository is `main`. Please submit all pull requests to the `main` branch. ## Bug reports and feature requests For bug reports and feature requests, please open an issue on the -[GitHub issue tracker](https://github.com/cmelab/flowerMD/issues). +[GitHub issue tracker](https://github.com/cmelab/flowerMD/issues). If you are reporting a bug, please include the following information: - A short description of the bug @@ -27,10 +27,10 @@ interested in contributing code, please follow the steps below: - Create a new branch for your feature/bug fix - Create the `flowermd` conda environment using the `environment-cpu.yml` or `environment-gpu.yml` file - Make your changes -- Install the latest version of pre-commit using `conda install -c conda-forge pre-commit` and run `pre-commit install` in the root directory of the repository +- Install the latest version of pre-commit using `conda install -c conda-forge pre-commit` and run `pre-commit install` in the root directory of the repository - Commit your changes and make sure all the pre-commit hooks pass - Push your changes to your fork and create a pull request - Assign the pull request to a reviewer and wait for the reviewers feedback New functionalities should be covered by unit tests. If you are adding a new -function/feature/class please follow the existing style for docstrings. \ No newline at end of file +function/feature/class please follow the existing style for docstrings. From e1114a2842be6f3b250e9066b9c4684dda796e21 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 23 Oct 2023 18:19:23 +0000 Subject: [PATCH 6/6] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/psf/black: 23.9.1 → 23.10.0](https://github.com/psf/black/compare/23.9.1...23.10.0) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c07413d5..cbb73c91 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -18,7 +18,7 @@ repos: - id: trailing-whitespace exclude: 'flowermd/tests/assets/.* | flowermd/assets/.*' - repo: https://github.com/psf/black - rev: 23.9.1 + rev: 23.10.0 hooks: - id: black args: [ --line-length=80 ]