namdtools 0.2.3.post0.dev4__tar.gz → 0.4.0__tar.gz

namdtools-0.2.3.post0.dev4/README.rst → namdtools-0.4.0/PKG-INFO

@@ -1,7 +1,19 @@
+Metadata-Version: 2.2
+Name: namdtools
+Version: 0.4.0
+Summary: A Python interface to NAMD
+Home-page: https://www.lockhartlab.org
+Author: C. Lockhart
+Author-email: clockha2@gmu.edu
+Requires-Dist: numpy
+Requires-Dist: pandas
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: home-page
+Dynamic: requires-dist
+Dynamic: summary
 
-.. image:: namdtools.svg
-   :alt: namdtools
-   :height: 200
 
 a Python interface to NAMD
 http://www.ks.uiuc.edu/Research/namd/
@@ -12,13 +24,6 @@ http://www.ks.uiuc.edu/Research/namd/
 .. image:: https://img.shields.io/pypi/v/namdtools
    :target: https://pypi.org/project/namdtools/
 
-.. image:: https://img.shields.io/codecov/c/github/clockhart/namdtools/master
-   :target: https://codecov.io/gh/clockhart/namdtools
-
-..
-   *dev:*
-   <nobr><img src="https://img.shields.io/travis/com/lockhartlab/molecular/dev"  alt="build-status-dev"/></nobr>
-   <nobr><img src="https://img.shields.io/codecov/c/github/lockhartlab/molecular/dev" alt="coverage-dev"/></nobr>
 
 note that this package is **still in development**
 at this stage, I'm only building thing as they come to mind  
@@ -34,3 +39,4 @@ similar packages:
 https://github.com/sunhwan/NAMD-replica
 https://github.com/bio-phys/MDBenchmark
 https://github.com/radakb/pynamd/
+

namdtools-0.4.0/README.rst

@@ -0,0 +1,26 @@
+
+a Python interface to NAMD
+http://www.ks.uiuc.edu/Research/namd/
+
+..
+   master
+
+.. image:: https://img.shields.io/pypi/v/namdtools
+   :target: https://pypi.org/project/namdtools/
+
+
+note that this package is **still in development**
+at this stage, I'm only building thing as they come to mind  
+version 1.0 will be the first major release  
+until then, consider this code heavily volatile
+
+yet, install simply by calling `pip install namdtools` or `pip install --pre namdtools` for the latest development
+release.
+
+we endeavor to follow https://scikit-learn.org/stable/developers/performance.html
+
+similar packages:
+https://github.com/sunhwan/NAMD-replica
+https://github.com/bio-phys/MDBenchmark
+https://github.com/radakb/pynamd/
+

namdtools-0.4.0/namdtools/__init__.py

@@ -0,0 +1,11 @@
+from .pme import *
+from .read import *
+
+__all__ = [
+    "get_pme_size",
+    "read_log",
+]
+
+from . import _version
+
+__version__ = _version.get_versions()["version"]

{namdtools-0.2.3.post0.dev4 → namdtools-0.4.0}/namdtools/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2022-12-30T19:31:30-0500",
+ "date": "2025-11-02T15:37:36-0500",
  "dirty": false,
  "error": null,
- "full-revisionid": "7734c79da634b2dd5873fb690843e903be99cd0a",
- "version": "0.2.3.post0.dev4"
+ "full-revisionid": "d1a589a0893aa83ce1286eb0642f201ddd8b0694",
+ "version": "0.4.0"
 }
 '''  # END VERSION_JSON
 

{namdtools-0.2.3.post0.dev4/namdtools/analysis → namdtools-0.4.0/namdtools}/pme.py

@@ -1,9 +1,3 @@
-"""
-pme.py
-written in Python3
-author: C. Lockhart <chrisblockhart@gmail.com>
-"""
-
 import numpy as np
 
 
@@ -45,5 +39,5 @@ def get_pme_size(a):
     return a
 
 
-if __name__ == '__main__':
-    print(get_pme_size(68.))
+if __name__ == "__main__":
+    print(get_pme_size(68.0))

namdtools-0.4.0/namdtools/read.py

@@ -0,0 +1,36 @@
+import pandas as pd
+
+
+# Read output from NAMD run
+def read_log(fname):
+    r"""
+    Read output from NAMD.
+
+    Parameters
+    ----------
+    fname : str
+        Name of NAMD output file.
+
+    Returns
+    -------
+    DataFrame
+    """
+
+    # Initialize log info
+    columns = None
+    records = []
+
+    # Read through log file and extract energy records
+    with open(fname, "r") as buf:
+        for line in buf:
+            # Read first ETITLE
+            if columns is None and line.startswith("ETITLE"):
+                columns = line.lower().split()[1:]
+
+            # Save each energy record
+            if line.startswith("ENERGY"):
+                records.append(line.split()[1:])
+
+    # Return
+    return pd.DataFrame(records, columns=columns).set_index(columns[0]).astype(float)
+

namdtools-0.4.0/namdtools.egg-info/PKG-INFO

@@ -0,0 +1,42 @@
+Metadata-Version: 2.2
+Name: namdtools
+Version: 0.4.0
+Summary: A Python interface to NAMD
+Home-page: https://www.lockhartlab.org
+Author: C. Lockhart
+Author-email: clockha2@gmu.edu
+Requires-Dist: numpy
+Requires-Dist: pandas
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: home-page
+Dynamic: requires-dist
+Dynamic: summary
+
+
+a Python interface to NAMD
+http://www.ks.uiuc.edu/Research/namd/
+
+..
+   master
+
+.. image:: https://img.shields.io/pypi/v/namdtools
+   :target: https://pypi.org/project/namdtools/
+
+
+note that this package is **still in development**
+at this stage, I'm only building thing as they come to mind  
+version 1.0 will be the first major release  
+until then, consider this code heavily volatile
+
+yet, install simply by calling `pip install namdtools` or `pip install --pre namdtools` for the latest development
+release.
+
+we endeavor to follow https://scikit-learn.org/stable/developers/performance.html
+
+similar packages:
+https://github.com/sunhwan/NAMD-replica
+https://github.com/bio-phys/MDBenchmark
+https://github.com/radakb/pynamd/
+

namdtools-0.4.0/namdtools.egg-info/SOURCES.txt

@@ -0,0 +1,14 @@
+README.rst
+setup.cfg
+setup.py
+versioneer.py
+namdtools/__init__.py
+namdtools/_version.py
+namdtools/pme.py
+namdtools/read.py
+namdtools.egg-info/PKG-INFO
+namdtools.egg-info/SOURCES.txt
+namdtools.egg-info/dependency_links.txt
+namdtools.egg-info/requires.txt
+namdtools.egg-info/top_level.txt
+namdtools.egg-info/zip-safe

namdtools-0.4.0/namdtools.egg-info/requires.txt

@@ -0,0 +1,2 @@
+numpy
+pandas

{namdtools-0.2.3.post0.dev4 → namdtools-0.4.0}/setup.cfg

@@ -1,5 +1,5 @@
 [versioneer]
-vcs = git
+VCS = git
 style = pep440-pre
 versionfile_source = namdtools/_version.py
 versionfile_build = namdtools/_version.py

namdtools-0.4.0/setup.py

@@ -0,0 +1,32 @@
+
+from setuptools import setup
+import versioneer
+
+
+# Read in long description
+with open('README.rst', 'r') as buf:
+    long_description = buf.read()
+
+# Read in requirements.txt
+with open('requirements.txt', 'r') as buf:
+    requirements = buf.read().splitlines()
+
+
+# Setup
+setup(
+    name='namdtools',
+    version=versioneer.get_version(),
+    cmdclass=versioneer.get_cmdclass(),
+    author='C. Lockhart',
+    author_email='clockha2@gmu.edu',
+    description='A Python interface to NAMD',
+    long_description=long_description,
+    # long_description_content_type='text/markdown',
+    url="https://www.lockhartlab.org",
+    packages=[
+        'namdtools',
+    ],
+    install_requires=requirements,
+    include_package_data=True,
+    zip_safe=True,
+)

namdtools-0.2.3.post0.dev4/.gitattributes

@@ -1 +0,0 @@
-namdtools/_version.py export-subst

namdtools-0.2.3.post0.dev4/.github/workflows/build.yml

@@ -1,49 +0,0 @@
-
-name: build
-
-on:
-  push
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v2
-      with:
-        fetch-depth: 0
-
-    - name: Setup Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.8'
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install --upgrade numpy
-        pip install -r requirements_dev.txt
-        pip install -r requirements.txt
-
-    - name: Install package
-      run: |
-        python -m pip install -e .
-
-    - name: Test
-      run: |
-        echo 0
-
-    - name: Make documentation
-      run: |
-        cd docs
-        rm -rf source/api/generated
-        rm -rf build
-        make html
-
-    - name: Sync with github
-      run: |
-        git config --local user.name "github-actions"
-        git config --local user.email "github-actions@github.com"
-        git add -A
-        git commit --amend --no-edit
-        git push -f

namdtools-0.2.3.post0.dev4/.gitignore

@@ -1,9 +0,0 @@
-/build/
-/dist/
-.hypothesis/
-.hypothesis/*
-/.idea/
-/namdtools.egg-info/
-__pycache__/
-__pycache__/*
-/_scripts/

namdtools-0.2.3.post0.dev4/.scripts/README

@@ -1,4 +0,0 @@
-
-1. Tag
-2. Deploy
-3. Push

namdtools-0.2.3.post0.dev4/.scripts/get_version.sh

@@ -1,6 +0,0 @@
-
-# meant to be run from root dir
-
-version=$(python -c "import versioneer; print(versioneer.get_version())")
-echo $version | sed 's/+.*//g' | sed 's/\./\ /g'  
-

namdtools-0.2.3.post0.dev4/.scripts/make_docs.sh

@@ -1,6 +0,0 @@
-
-cd docs
-rm -rf source/api/generated
-rm -rf build
-make clean
-make html

namdtools-0.2.3.post0.dev4/.scripts/pypi.sh

@@ -1,8 +0,0 @@
-
-# python setup.py register sdist upload
-
-
-python setup.py sdist bdist_wheel
-twine check dist/*
-twine upload dist/*
-

namdtools-0.2.3.post0.dev4/.scripts/temp

@@ -1,16 +0,0 @@
-
-    - name: Make documentation
-      run: |
-        cd docs
-        rm -rf source/api/generated
-        rm -rf build
-        make clean
-        make html
-
-    - name: Sync with github
-      run: |
-        git config --local user.name "github-actions"
-        git config --local user.email "github-actions@github.com"
-        git add -A
-        git commit --amend --no-edit
-        git push -f

namdtools-0.2.3.post0.dev4/.scripts/update_major.sh

@@ -1,8 +0,0 @@
-
-# meant to be run in root directory
-
-read major minor patch <<< $(bash .scripts/get_version.sh)
-major=$(expr $major + 1)
-git tag ${major}.0.0
-
-

namdtools-0.2.3.post0.dev4/.scripts/update_minor.sh

@@ -1,8 +0,0 @@
-
-# meant to be run in root directory
-
-read major minor patch <<< $(bash .scripts/get_version.sh)
-minor=$(expr $minor + 1)
-git tag ${major}.${minor}.0
-
-

namdtools-0.2.3.post0.dev4/.scripts/update_patch.sh

@@ -1,8 +0,0 @@
-
-# meant to be run in root directory
-
-read major minor patch <<< $(bash .scripts/get_version.sh)
-patch=$(expr $patch + 1)
-git tag ${major}.${minor}.${patch}
-
-

namdtools-0.2.3.post0.dev4/MANIFEST.in

@@ -1,3 +0,0 @@
-recursive-include namdtools *.c *.pyf *.f90 *.pyx *.yml
-include requirements.txt
-include version.yml

namdtools-0.2.3.post0.dev4/PKG-INFO

@@ -1,46 +0,0 @@
-Metadata-Version: 1.0
-Name: namdtools
-Version: 0.2.3.post0.dev4
-Summary: A Python interface to NAMD
-Home-page: https://www.lockhartlab.org
-Author: C. Lockhart
-Author-email: clockha2@gmu.edu
-License: UNKNOWN
-Description: 
-        .. image:: namdtools.svg
-           :alt: namdtools
-           :height: 200
-        
-        a Python interface to NAMD
-        http://www.ks.uiuc.edu/Research/namd/
-        
-        ..
-           master
-        
-        .. image:: https://img.shields.io/pypi/v/namdtools
-           :target: https://pypi.org/project/namdtools/
-        
-        .. image:: https://img.shields.io/codecov/c/github/clockhart/namdtools/master
-           :target: https://codecov.io/gh/clockhart/namdtools
-        
-        ..
-           *dev:*
-           <nobr><img src="https://img.shields.io/travis/com/lockhartlab/molecular/dev"  alt="build-status-dev"/></nobr>
-           <nobr><img src="https://img.shields.io/codecov/c/github/lockhartlab/molecular/dev" alt="coverage-dev"/></nobr>
-        
-        note that this package is **still in development**
-        at this stage, I'm only building thing as they come to mind  
-        version 1.0 will be the first major release  
-        until then, consider this code heavily volatile
-        
-        yet, install simply by calling `pip install namdtools` or `pip install --pre namdtools` for the latest development
-        release.
-        
-        we endeavor to follow https://scikit-learn.org/stable/developers/performance.html
-        
-        similar packages:
-        https://github.com/sunhwan/NAMD-replica
-        https://github.com/bio-phys/MDBenchmark
-        https://github.com/radakb/pynamd/
-        
-Platform: UNKNOWN

namdtools-0.2.3.post0.dev4/README.md

@@ -1,28 +0,0 @@
-<img src="namdtools.svg" alt="namdtools" height="200px">
-
-a Python interface to NAMD  
-http://www.ks.uiuc.edu/Research/namd/
-
-<!--*master:*-->
-<span style="white-space: nowrap;">
-    <a href="https://pypi.org/project/namdtools/"><img src="https://img.shields.io/pypi/v/namdtools" /></a>
-    <a href="https://travis-ci.com/github/LockhartLab/namdtools"><img src="https://img.shields.io/travis/com/lockhartlab/namdtools/master" /></a>
-    <a href="https://codecov.io/gh/LockhartLab/namdtools"><img src="https://img.shields.io/codecov/c/github/lockhartlab/namdtools/master" /></a>
-</span>
-
-<hr>
-
-note that this package is **still in development**  
-at this stage, I'm only building thing as they come to mind  
-version 1.0 will be the first major release  
-until then, consider this code heavily volatile
-
-yet, install simply by calling ```pip install namdtools```
-
-<hr>
-
-Related Packages
-----------------
-https://github.com/sunhwan/NAMD-replica  
-https://github.com/bio-phys/MDBenchmark  
-https://github.com/radakb/pynamd/

namdtools-0.2.3.post0.dev4/docs/Makefile

@@ -1,20 +0,0 @@
-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line, and also
-# from the environment for the first two.
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
-BUILDDIR      = build
-
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

namdtools-0.2.3.post0.dev4/docs/build/html/.buildinfo

@@ -1,4 +0,0 @@
-# Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 80c9741e8b910e1317949066c8373a00
-tags: 645f666f9bcd5a90fca523b33c5a78b7

namdtools-0.2.3.post0.dev4/docs/build/html/_images/namdtools.svg

@@ -1 +0,0 @@
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namdtools-0.2.3.post0.dev4/docs/build/html/_modules/index.html

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