Merge pull request #23 from QTC-UMD/v2rc

Rydiqule v2.0.0 beta release

.github/workflows/checks.yml

@@ -41,4 +41,26 @@ jobs:
 
       - name: Run Unit Tests
         run: |
-          pytest ./tests/ -m "not high_memory and not slow"
+          pytest . -m "not high_memory and not slow"
+
+  pytest-np2:
+    name: Unit Tests with Numpy 2
+    runs-on: ubuntu-latest
+    if: github.repository_owner == 'QTC-UMD' || github.repository_owner == 'naqslab'
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install Rydiqule and Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[tests]
+
+      - name: Run Unit Tests
+        run: |
+          pytest . -m "not high_memory and not slow and not backend"

.gitignore

@@ -74,13 +74,7 @@ instance/
 
 # Sphinx documentation
 docs/source/api/_autosummary
-docs/source/_examples
-docs/source/_intro_nbs
-# track the output pdf
 docs/build/*
-!docs/build/latex
-docs/build/latex/*
-!docs/build/latex/rydiqule.pdf
 
 # PyBuilder
 target/
@@ -166,3 +160,4 @@ Untitled.ipynb
 profiling
 *.pkl
 sensor_inventory/*.pkl
+.vscode/settings.json

README.md

@@ -9,6 +9,7 @@ It also functions as a general master equation solver based on the semi-classica
 [![Python Version](https://img.shields.io/pypi/pyversions/rydiqule.svg)](https://python.org)
 [![License](https://img.shields.io/pypi/l/rydiqule.svg)](https://github.com/QTC-UMD/rydiqule/raw/main/LICENSE)
 [![Docs](https://readthedocs.org/projects/rydiqule/badge/?version=latest)](https://rydiqule.readthedocs.io/en/latest)
+[![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.cpc.2023.108952-goldenrod.svg)](https://doi.org/10.1016/j.cpc.2023.108952)
 
 ### Please cite as
 
@@ -19,142 +20,8 @@ RydIQule: A Graph-based paradigm for modeling Rydberg and atomic sensors,
 
 ## Installation
 
-Installation is done via pip or conda.
-See below for detailed instructions.
-
-In all cases, it is highly recommended to install rydiqule in a virtual environment.
-
-### Conda installation (recommended)
-
-Installation via conda is recommended for rydiqule.
-It handles dependency installation as well as a virtual environment to ensure packages do not conflict with other usages on the same system.
-Finally, the `numpy` provided by anaconda has been compiled against optimized BLAS/LAPACK implementations, which results in much better performance in rydiqule itself.
-
-Assuming you have not already created a separate environment for RydIQule (recommended), run the following to create a new environment:
-```shell
-(base) ~/> conda create -n rydiqule python=3.11
-(base) ~/> conda activate rydiqule
-```
-RydIQule currently requires python >3.8.
-For a new installation, it is recommended to use the newest supported python.
-
-Now install via rydiqule's anaconda channel.
-This channel provides rydiqule as well as its dependencies that are not available in the default anaconda channel.
-If one of these dependencies is outdated, please raise an issue with the [vendoring repository](https://github.com/QTC-UMD/rydiqule-vendored-conda-builds).
-```shell
-(rydiqule) ~/> conda install -c rydiqule rydiqule
-```
-
-If you would like to install rydiqule in editable mode to locally modify its source,
-this must be done using pip.
-Follow the above to install rydiqule and its dependencies,
-then run the following to uninstall rydiqule as provided by conda
-and install the editable local repository.
-```shell
-(rydiqule) ~/> conda remove rydiqule --force
-# following must be run from root of local repository
-(rydiqule) ~/> pip install -e .
-```
-
-Note that editable installations require `git`.
-This can be provided by a system-wide installation or via conda in the virtual environment (`conda install git`).
-
-While rydiqule is a pure python package (ie it is platform independent), its core dependency ARC is not.
-If a pre-built package of ARC is not available for your platform in our anaconda channel,
-you will need to install ARC via `pip` to build it locally before installing `rydiqule`.
-To see what architectures are supported, please see the [vendoring repository](https://github.com/QTC-UMD/rydiqule-vendored-conda-builds).
-
-
-### Pure pip installation
-
-To install normally, run:
-```shell
-pip install rydiqule
-```
-This command will use pip to install all necessary dependencies.
-
-To install in an editable way (which allows edits of the source code),
-run the following from the root directory of the cloned repository:
-```shell
-pip install -e .
-```
-
-Editable installation requires `git` to be installed.
-
-### Confirm installation
-
-Proper installation can be confirmed by executing the following commands in a python terminal.
-```shell
->>> import rydiqule as rq
->>> rq.about()
-
-        Rydiqule
-    ================
-
-Rydiqule Version:     1.1.0
-Installation Path:    ~\Miniconda3\envs\rydiqule\lib\site-packages\rydiqule
-
-      Dependencies
-    ================
-
-NumPy Version:        1.24.3
-SciPy Version:        1.10.1
-Matplotlib Version:   3.7.1
-ARC Version:          3.3.0
-Python Version:       3.9.16
-Python Install Path:  ~\Miniconda3\envs\rydiqule
-Platform Info:        Windows (AMD64)
-CPU Count:            12
-Total System Memory:  128 GB
-```
-
-### Updating an existing installation
-
-Upgrading an existing installation is simple.
-Simply run the appropriate upgrade command for the installation method used.
-
-For conda installations, run the following command to upgrade rydiqule
-```shell
-conda upgrade rydiqule
-```
-
-For `pip`, you can use the installation command to upgrade.
-Optionally, include the update flag to greedily update dependencies as well.
-```shell
-pip install -U rydiqule
-```
-This command will also install any new dependencies that are required.
-
-If using an editable install, simply replacing the files in the same directory is sufficient.
-Though it is recommended to also run the appropriate pip update command as well to capture updated dependencies.
-```shell
-pip install -U -e .
-```
-
-### Dependencies
-
-This package requires installation of the excellent [ARC](https://github.com/nikolasibalic/ARC-Alkali-Rydberg-Calculator) package, which is used to get Rydberg atomic properties.
-It also requires other standard computation dependenices, such as `numpy`, `scipy`, `matplotlib`, etc.
-These dependencies will be automatically installed if not already present.
-
-Rydiqule's performance does depend on these depedencies.
-In particular, `numpy` can be compiled with a variety of backends that implements
-BLAS and LAPACK routines that can have different performance for different computer architectures.
-When using Windows, it is recommended to install `numpy` from conda,
-which is built against the IntelMKL and has generally shown the best performance for Intel-based PCs.
-
-Optional timesolver backend dependencies include the [numbakit-ode](https://github.com/hgrecco/numbakit-ode)
-and [CyRK](https://github.com/jrenaud90/CyRK) packages.
-Both are available via `pip` or our anaconda channel.
-They can be installed automatically via the optional extras specification for the `pip` command.
-```shell
-pip install rydiqule[backends]
-```
-
-For conda installations, these dependencies must be installed manually.
-```shell
-conda install -c rydiqule CyRK numbakit-ode
-```
+Installation can be done via pip or conda.
+See the [documentation](https://rydiqule.readthedocs.io/en/latest/installation.html) for details.
 
 ## Documentation
 
@@ -163,8 +30,8 @@ PDF or EPUB formats of the documentation can be downloaded from the online docum
 
 ### Examples
 
-Example jupyter notebooks that demonstrate RydIQule can be found in the `examples` subdirectory.
-Printouts of these notebooks are available in the documentation as well.
+Example jupyter notebooks that demonstrate RydIQule can be found in the documentation,
+with back-links to download them directly from the github repository.
 
 ## Support
 
@@ -180,4 +47,4 @@ The github repository is for code distribution only.
 While we monitor it, 
 we will not directly respond to issues or pull requests posted to it.
 If you would like a response from the developers, please e-mail
-[email protected] or [email protected]
+[email protected] or [email protected]

docs/Makefile

@@ -7,12 +7,18 @@ SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = source
 BUILDDIR      = build
+AUTOSUMMARYDIR = source/api/_autosummary
 
 # Put it first so that "make" without argument is like "make help".
 help:
 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-.PHONY: help Makefile
+clean:
+	@echo "Removing autosummary directory"
+	@rm -rf $(AUTOSUMMARYDIR)
+	@$(SPHINXBUILD) -M clean "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help clean Makefile
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).

docs/make.bat

@@ -9,8 +9,10 @@ if "%SPHINXBUILD%" == "" (
 )
 set SOURCEDIR=source
 set BUILDDIR=build
+set AUTOSUMMARYDIR=source\api\_autosummary
 
 if "%1" == "" goto help
+if "%1" == "clean" goto clean
 
 %SPHINXBUILD% >NUL 2>NUL
 if errorlevel 9009 (
@@ -30,6 +32,12 @@ goto end
 
 :help
 %SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:clean
+echo Removing autosummary directory
+rmdir /s/q %AUTOSUMMARYDIR%
+%SPHINXBUILD% -M clean %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
 
 :end
 popd

docs/source/_templates/autosummary-module.rst

@@ -60,7 +60,9 @@
    :template: autosummary-module.rst
    :recursive:
 {% for item in modules %}
+{% if not item.endswith('conftest') %}
    {{ item }}
+{%- endif %}
 {%- endfor %}
 {% endif %}
 {% endblock %}