IMDReader removed from imdclient (#54)

* fix #53
* package now only contains imdclient
* remove IMDReader (moving to MDAnalysis)
   - IMDReader and StreamReaderBase has been removed from the main package
   - Tests for the IMDReader have been removed from the tests folder
   - package does not require MDAnalysis (except for testing)
* updated tests: uses custom MinimalReader for MD engine tests
* ensure that tests correctly test integration time step
* updated project files with changes in dependencies
* updated docs (changed all references to be imdclient as package name)
* updated AUTHORS
* updated CHANGELOG

---------

Co-authored-by: Amruthesh Thirumalaiswamy <amruthesht@users.noreply.github.com>
Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
Co-authored-by: Jennifer A. Clark <jennifer.a.clark13@gmail.com>
Co-authored-by: Lawson Woods <ljwoods2@asu.edu>
Co-authored-by: ljwoods2 <145226270+ljwoods2@users.noreply.github.com>

Author: 4 people

.github/workflows/gh-ci.yaml

@@ -45,11 +45,10 @@ jobs:
     needs: environment-config
     runs-on: ${{ matrix.os }}
     strategy:
-        fail-fast: false
-        matrix:
-          os: [macOS-latest, ubuntu-latest]
-          python-version: ["3.10", "3.11", "3.12"]
-          mdanalysis-version: ["latest"]
+      fail-fast: false
+      matrix:
+        os: [macOS-latest, ubuntu-latest]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v4
@@ -81,16 +80,7 @@ jobs:
         show-channel-urls: true
         miniconda-version: latest
 
-
-    - name: Install MDAnalysis version
-      uses: MDAnalysis/install-mdanalysis@main
-      with:
-        version: ${{ matrix.mdanalysis-version }}
-        install-tests: true
-        installer: conda
-        shell: bash -l {0} 
-      
-    - name: Install package
+    - name: Install imdclient
       run: |
         python --version
         python -m pip install .  --no-deps 
@@ -106,10 +96,10 @@ jobs:
     - name: Run IMDClient tests
       run: |
         pytest -n auto -v --cov=imdclient --cov-report=xml --color=yes imdclient/tests/test_imdclient.py
-  
-    - name: Run IMDReader tests
+
+    - name: Run package utilities tests
       run: |
-        pytest -n auto -v --cov=imdclient --cov-report=xml --color=yes imdclient/tests/test_imdreader.py
+        pytest -n auto -v --cov=imdclient --cov-report=xml --color=yes imdclient/tests/test_utils.py
 
     - name: codecov
       if: github.event_name != 'schedule'
@@ -174,14 +164,6 @@ jobs:
           show-channel-urls: true
           miniconda-version: latest
 
-      - name: Install MDAnalysis version
-        uses: MDAnalysis/install-mdanalysis@main
-        with:
-          version: latest
-          install-tests: true
-          installer: conda
-          shell: bash -l {0} 
-        
       - name: Install package
         run: |
           python --version

AUTHORS.md

@@ -4,7 +4,7 @@ IMDClient was created by Lawson in 2024.
 
 
 <!-- All contributing authors are listed in this file below.
-The repository history at https://github.com/becksteinlab/imdreader
+The repository history at https://github.com/becksteinlab/imdclient
 and the CHANGELOG show individual code contributions. -->
 
 ## Chronological list of authors
@@ -19,5 +19,8 @@ The rules for this file:
   * Don't ever delete anything
 -->
 
+**2025**
+- Amruthesh Thirumalaiswamy <@amruthesht>
+
 **2024**
 - Lawson <@ljwoods2>

CHANGELOG.md

@@ -20,15 +20,20 @@ The rules for this file:
 
 ### Authors
 <!-- GitHub usernames of contributors to this release -->
+@amruthesht @ljwoods2
 
 ### Added
 <!-- New added features -->
+* Updated installation instructions by @amruthesht in https://github.com/Becksteinlab/imdclient/pull/74
+* MD engine links updated in IMDClient documnetation by @amruthesht in https://github.com/Becksteinlab/imdclient/pull/73
+* Parse input files for DT when not in traj by @ljwoods2 in https://github.com/Becksteinlab/imdclient/pull/71
 
 ### Fixed
 <!-- Bug fixes -->
 
 ### Changed
 <!-- Changes in existing functionality -->
+* IMDReader removed from imdclient by @amruthesht in https://github.com/Becksteinlab/imdclient/pull/54
 
 ### Deprecated
 <!-- Soon-to-be removed features -->
@@ -38,6 +43,29 @@ The rules for this file:
 
 
 
+## [v0.1.5-alpha] - 2025-06-24
+
+### Authors
+<!-- GitHub usernames of contributors to this release -->
+@orbeckst @amruthesht @hcho38 @ljwoods2
+
+### Added
+<!-- New added features -->
+* NAMD Testing with private image + Docs by @ljwoods2 in https://github.com/Becksteinlab/imdclient/pull/46
+* Lammps usage docs by @ljwoods2 in https://github.com/Becksteinlab/imdclient/pull/49
+* Instructions for various namd builds by @amruthesht in https://github.com/Becksteinlab/imdclient/pull/51
+* chore: added client.py files and cleaned uo output data from examples by @amruthesht in https://github.com/Becksteinlab/imdclient/pull/52
+* add codecov token to workflow by @orbeckst in https://github.com/Becksteinlab/imdclient/pull/60
+* add sphinx.configuration for RTD by @orbeckst in https://github.com/Becksteinlab/imdclient/pull/62
+* Updated CHANGELOG based on the release notes of IMDClient by @hcho38 in https://github.com/Becksteinlab/imdclient/pull/67
+* `IMD_TIME` packet definitions modified by @amruthesht in https://github.com/Becksteinlab/imdclient/pull/68
+
+### Changed
+<!-- Changes in existing functionality -->
+* Run all simulation enegine tests regardless of failed tests by @amruthesht in https://github.com/Becksteinlab/imdclient/pull/69
+
+
+
 ## [v0.1.4] - 2024-12-13
 
 ### Authors

README.md

@@ -5,25 +5,23 @@ IMDClient
 | **Latest release** | [![Last release tag][badge_release]][url_latest_release] ![GitHub commits since latest release (by date) for a branch][badge_commits_since]  [![Documentation Status][badge_docs]][url_docs]|
 | :----------------- | :------- |
 | **Status**         | [![GH Actions Status][badge_actions]][url_actions] [![codecov][badge_codecov]][url_codecov] |
-| **Community**      | [![License: MIT][badge_license]][url_license]  [![Powered by MDAnalysis][badge_mda]][url_mda]|
+| **Community**      | [![License: MIT][badge_license]][url_license]
 
 [badge_actions]: https://github.com/becksteinlab/imdclient/actions/workflows/gh-ci.yaml/badge.svg
 [badge_codecov]: https://codecov.io/gh/becksteinlab/imdclient/branch/main/graph/badge.svg
 [badge_commits_since]: https://img.shields.io/github/commits-since/becksteinlab/imdclient/latest
 [badge_docs]: https://readthedocs.org/projects/imdclient/badge/?version=latest
 [badge_license]: https://img.shields.io/badge/License-MIT-blue.svg
-[badge_mda]: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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
 [badge_release]: https://img.shields.io/github/release-pre/becksteinlab/imdclient.svg
 [url_actions]: https://github.com/becksteinlab/imdclient/actions?query=branch%3Amain+workflow%3Agh-ci
 [url_codecov]: https://codecov.io/gh/becksteinlab/imdclient/branch/main
 [url_docs]: https://imdclient.readthedocs.io/en/latest/?badge=latest
 [url_latest_release]: https://github.com/becksteinlab/imdclient/releases
 [url_license]: https://opensource.org/license/mit
-[url_mda]: https://www.mdanalysis.org
 
 Receiver for [IMDv3 protocol](https://imdclient.readthedocs.io/en/latest/protocol_v3.html) from simulation engines like Gromacs, LAMMPS, and NAMD.
 
-IMDClient is bound by a [Code of Conduct](https://github.com/becksteinlab/imdreader/blob/main/CODE_OF_CONDUCT.md).
+IMDClient is bound by a [Code of Conduct](https://github.com/becksteinlab/imdclient/blob/main/CODE_OF_CONDUCT.md).
 
 ### Installation
 
@@ -110,7 +108,7 @@ pip install ".[test,doc]"
 The IMDClient source code is hosted at https://github.com/becksteinlab/imdclient
 and is available under the MIT license (see the file [LICENSE](https://github.com/becksteinlab/imdclient/blob/main/LICENSE)).
 
-Copyright (c) 2024, Lawson
+Copyright (c) 2024-2025, imdclient [AUTHORS](https://github.com/Becksteinlab/imdclient/blob/main/AUTHORS.md)
 
 
 #### Acknowledgements

devtools/conda-envs/test_env.yaml

@@ -8,17 +8,17 @@ dependencies:
   - pip
 
   # MDAnalysis
-  - MDAnalysis>=2.7.0
+  - MDAnalysis
 
   # Testing
   - pytest
   - pytest-cov
   - pytest-xdist
   - codecov
-  - MDAnalysisTests>=2.7.0
+  - MDAnalysisTests
   - docker-py
 
   # Pip-only installs
-  #- pip:
+  # - pip:
   #  - codecov
 

docs/requirements.yaml

@@ -1,14 +1,11 @@
-name: imdreader-docs
+name: imdclient-docs
 channels:
-
   - conda-forge
-
 dependencies:
     # Base depends
   - python
-  - pip
-
   - mdanalysis-sphinx-theme >=1.0.1
+  - pip
   - sphinxcontrib-bibtex
     # Pip-only installs
-  #- pip:
+    # - pip:

docs/source/api.rst

@@ -1,5 +1,4 @@
 API Documentation
 =================
 
-.. automodule:: imdclient.IMD
 .. automodule:: imdclient.IMDClient

docs/source/index.rst

@@ -1,11 +1,14 @@
-.. imdclient documentation master file, created by
-   sphinx-quickstart on Thu Mar 15 13:55:56 2018.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
 Welcome to IMDClient's documentation!
 =========================================================
 
+IMDClient is a Python-based client library designed to interact with simulation engines making interactive molecular dynamics
+(IMD) possible. It provides tools for communicating with the IMDv2 and new IMDv3 protocols, enabling seamless integration
+between its API with simulation engines such as NAMD, LAMMPS, and GROMACS. Users can leverage this library to build
+applications that interact with the IMD system efficiently, e.g., MDAnalysis IMDReader. IMDv3 has been standardized across
+supported simulation engines with regard to transmitted data and is processed in IMDClient to provide consistent
+`units <protocol_v3.html#units>`_. See `IMDv3 Protocol <protocol_v3.html>`_ for more details. IMDClient is ideal for
+developers looking to produce on-the-fly analysis, avoiding storage of large trajectories.
+
 .. toctree::
    :maxdepth: 2
    :caption: Contents: