pulserver 0.1.0__tar.gz → 0.1.2__tar.gz

pulserver-0.1.2/.github/workflows/docker.yml

@@ -0,0 +1,39 @@
+name: Build and Push Docker Image
+
+on:
+    push:
+      tags:
+        - 'v[0-9]+.[0-9]+.[0-9]+'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      # Checkout the repository
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      # Set up Docker Buildx
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      # Log in to Docker Hub
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_TOKEN }}
+
+      # Build and push the Docker image
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: ./docker
+          file: ./docker/Dockerfile
+          push: true
+          tags: ${{ secrets.DOCKER_USERNAME }}/pulserver:latest
+
+      # Optionally, log out of Docker Hub
+      - name: Log out of Docker Hub
+        run: docker logout

pulserver-0.1.0/.github/workflows/test-cicd.yml → pulserver-0.1.2/.github/workflows/test-ci.yml

@@ -1,4 +1,4 @@
-name: CI/CD
+name: CI-CD
 
 on: 
   push:
@@ -9,11 +9,10 @@ on:
 jobs:
   test:
     runs-on: ubuntu-latest
-    needs: [test]
-
+    
     strategy:
       matrix:
-        python-version: [3.10, 3.12]  # Specify the desired Python versions
+        python-version: [3.11, 3.12]  # Specify the desired Python versions
 
     steps:
       - name: Checkout code
@@ -29,29 +28,38 @@ jobs:
           pip install .[test]
 
       - name: Run tests
-        run: pytest --cov --cov-report=xml tests
-		
+        run: pytest --cov --cov-report=xml tests	
+      
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v4.0.1
         with:
           token:  ${{ secrets.CODECOV_TOKEN }}
-          slug: INFN-MRI/pulserver
-		  
+          slug: INFN-MRI/pulserver		  
+  
   docs:
     runs-on: ubuntu-20.04
     needs: [test]
     steps:
-      - name: Get the docs_build artifact
-        uses: actions/download-artifact@v4
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
-          name: docs_final
-          path: docs_build
-          run-id: ${{ github.event.workflow_run.id }}
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-		  
+          python-version: "3.10"
+      
+      - name: Install dependencies
+        run: |
+          pip install .[doc]
+          python -m pip install -r docs/requirements.txt
+      
+      - name: Build API documentation
+        run: |
+          python -m sphinx docs docs_build
+      
       - name: Display structure of docs
-        run: ls -R docs_build/
-		  
+        run: ls -R docs_build/	  
+      
       - name: Deploy to GitHub Pages
         uses: peaceiris/actions-gh-pages@v4
         with:
@@ -60,6 +68,3 @@ jobs:
           destination_dir: .  # Ensure you deploy to the root of the gh-pages branch
           publish_branch: gh-pages
           keep_files: false
-		
-	
-		

{pulserver-0.1.0 → pulserver-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pulserver
-Version: 0.1.0
+Version: 0.1.2
 Summary: A PyPulseq-based client/server MR sequence design toolbox.
 Author-email: Matteo Cencini <matteo.cencini@gmail.com>
 Project-URL: Homepage, https://github.com/INFN-MRI/pulserver
@@ -16,6 +16,7 @@ Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.10
 Description-Content-Type: text/x-rst
 License-File: LICENSE.txt
+Requires-Dist: pyyaml
 Requires-Dist: numpy<2.0
 Requires-Dist: scipy<1.14
 Requires-Dist: numba
@@ -39,9 +40,34 @@ Requires-Dist: pydata-sphinx-theme; extra == "doc"
 Requires-Dist: myst-nb; extra == "doc"
 Requires-Dist: matplotlib; extra == "doc"
 Requires-Dist: mrtwin; extra == "doc"
+Requires-Dist: sphinx-copybutton; extra == "doc"
 
 Pulserver
 =========
+|Coverage| |CI/CD| |License| |Codefactor| |Sphinx| |PyPi| |Black| |PythonVersion|
+
+.. |Coverage| image:: https://codecov.io/gh/INFN-MRI/pulserver/graph/badge.svg?token=qtB53xANwI 
+ :target: https://codecov.io/gh/INFN-MRI/pulserver
+
+.. |CI/CD| image:: https://github.com/INFN-MRI/pulserver/workflows/CI-CD/badge.svg
+   :target: https://github.com/INFN-MRI/pulserver
+
+.. |License| image:: https://img.shields.io/github/license/INFN-MRI/pulserver
+   :target: https://github.com/INFN-MRI/pulserver/blob/main/LICENSE.txt
+
+.. |Codefactor| image:: https://www.codefactor.io/repository/github/INFN-MRI/pulserver/badge
+   :target: https://www.codefactor.io/repository/github/INFN-MRI/pulserver
+
+.. |Sphinx| image:: https://img.shields.io/badge/docs-Sphinx-blue
+   :target: https://infn-mri.github.io/pulserver
+
+.. |PyPi| image:: https://img.shields.io/pypi/v/pulserver
+   :target: https://pypi.org/project/pulserver
+
+.. |Black| image:: https://img.shields.io/badge/style-black-black
+
+.. |PythonVersion| image:: https://img.shields.io/badge/Python-%3E=3.10-blue?logo=python&logoColor=white
+   :target: https://python.org
 
 Pulserver is a high-level wrapper over PyPulseq. It is designed to 
 improve MR sequence code organization and provide a bridge

pulserver-0.1.2/README.rst

@@ -0,0 +1,77 @@
+Pulserver
+=========
+|Coverage| |CI/CD| |License| |Codefactor| |Sphinx| |PyPi| |Black| |PythonVersion|
+
+.. |Coverage| image:: https://codecov.io/gh/INFN-MRI/pulserver/graph/badge.svg?token=qtB53xANwI 
+ :target: https://codecov.io/gh/INFN-MRI/pulserver
+
+.. |CI/CD| image:: https://github.com/INFN-MRI/pulserver/workflows/CI-CD/badge.svg
+   :target: https://github.com/INFN-MRI/pulserver
+
+.. |License| image:: https://img.shields.io/github/license/INFN-MRI/pulserver
+   :target: https://github.com/INFN-MRI/pulserver/blob/main/LICENSE.txt
+
+.. |Codefactor| image:: https://www.codefactor.io/repository/github/INFN-MRI/pulserver/badge
+   :target: https://www.codefactor.io/repository/github/INFN-MRI/pulserver
+
+.. |Sphinx| image:: https://img.shields.io/badge/docs-Sphinx-blue
+   :target: https://infn-mri.github.io/pulserver
+
+.. |PyPi| image:: https://img.shields.io/pypi/v/pulserver
+   :target: https://pypi.org/project/pulserver
+
+.. |Black| image:: https://img.shields.io/badge/style-black-black
+
+.. |PythonVersion| image:: https://img.shields.io/badge/Python-%3E=3.10-blue?logo=python&logoColor=white
+   :target: https://python.org
+
+Pulserver is a high-level wrapper over PyPulseq. It is designed to 
+improve MR sequence code organization and provide a bridge
+between different Pulseq interpreter representations while providing
+a familiar interface to PyPulseq user.
+
+It also provide a server-based interface to enable online sequence design
+routines, e.g., using the MR scanner as a client.
+
+Features
+--------
+
+
+
+Installation
+------------
+Pulserver can be installed via pip:
+
+.. code-block:: bash
+
+    pip install pulserver
+
+Development
+-----------
+If you want to modifiy the Pulserver code base:
+
+.. code-block:: bash
+
+    git clone https://github.com/INFN-MRI/pulservert.git
+    pip install -e ./pulserver
+
+Usage
+-----
+
+TODO: add quick example
+
+Testing
+-------
+To run the tests, execute the following command in the terminal:
+
+.. code-block:: bash
+
+     pytest .
+
+License
+-------
+This project is licensed under the MIT License.
+
+Contributing
+------------
+Contributions are welcome! Please fork the repository and submit a pull request.

pulserver-0.1.2/docker/Dockerfile

@@ -0,0 +1,17 @@
+ARG BASE_IMAGE=ubuntu:22.04
+FROM ${BASE_IMAGE} as base
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+ARG PYTHON="python3.12"
+
+# install python and pulserver dependencies
+COPY install_pulserver.sh .
+RUN bash install_pulserver.sh
+RUN rm install_pulserver.sh
+
+# set user
+USER runner
+
+# set entrypoint
+ENTRYPOINT ["pulserver"]

pulserver-0.1.2/docker/install_pulserver.sh

@@ -0,0 +1,44 @@
+# define apt-get installation command
+APT_GET_INSTALL="apt-get install -yq --no-install-recommends"
+
+# update, qq: quiet
+apt-get update -qq
+
+# ensure certificates are up to date
+${APT_GET_INSTALL} --reinstall ca-certificates
+
+# base utilities
+${APT_GET_INSTALL} git software-properties-common gpg-agent
+
+# add repo for python installation
+add-apt-repository ppa:deadsnakes/ppa
+apt update -qq
+${APT_GET_INSTALL} $PYTHON-full
+
+# create alias for installed python version
+ln -s /usr/bin/$PYTHON /usr/local/bin/python
+ln -s /usr/bin/$PYTHON /usr/local/bin/python3
+
+# clone repo to get requirements
+git clone https://github.com/INFN-MRI/pulserver --depth 1 /opt/pulserver
+cd /opt/pulserver
+python -m ensurepip --upgrade
+python -m pip install --upgrade pip
+
+# create alias to ensure pip works in the same way as pip3
+ln -s /usr/local/bin/pip3 /usr/local/bin/pip
+
+# install mrpro and dependencies
+python -m pip install --upgrade --upgrade-strategy "eager" .
+
+# clean up
+rm -r /opt/pulserver
+apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# add user runner
+adduser --disabled-password --gecos "" --uid 1001 runner \
+    && groupadd docker --gid 123 \
+    && usermod -aG sudo runner \
+    && usermod -aG docker runner \
+    && echo "%sudo   ALL=(ALL:ALL) NOPASSWD:ALL" > /etc/sudoers \
+    && echo "Defaults env_keep += \"DEBIAN_FRONTEND\"" >> /etc/sudoers

{pulserver-0.1.0 → pulserver-0.1.2}/pyproject.toml

@@ -41,6 +41,7 @@ classifiers = [  # Optional
 ]
 
 dependencies = [
+"pyyaml",
 "numpy<2.0",
 "scipy<1.14",
 "numba",
@@ -55,7 +56,7 @@ dependencies = [
 [project.optional-dependencies] # Optional
 dev = ["black", "isort"]
 test = ["pytest", "pytest-black", "pytest-cov", "pytest-sugar", "pytest-xdist"]
-doc = ["sphinx", "pydata-sphinx-theme", "myst-nb", "matplotlib", "mrtwin"]
+doc = ["sphinx", "pydata-sphinx-theme", "myst-nb", "matplotlib", "mrtwin", "sphinx-copybutton"]
 # List URLs that are relevant to your project
 # This field corresponds to the "Project-URL" and "Home-Page" metadata fields:
 [project.urls]  # Optional
@@ -63,6 +64,9 @@ doc = ["sphinx", "pydata-sphinx-theme", "myst-nb", "matplotlib", "mrtwin"]
 "Bug Reports" = "https://github.com/INFN-MRI/pulserver/issues"
 "Source" = "https://github.com/INFN-MRI/pulserver"
 
+[project.scripts]  # Optional
+pulserver = "pulserver._cli:cli"
+
 [tool.setuptools.packages.find]
 where=["src"]
 

{pulserver-0.1.0 → pulserver-0.1.2}/src/pulserver/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.0'
-__version_tuple__ = version_tuple = (0, 1, 0)
+__version__ = version = '0.1.2'
+__version_tuple__ = version_tuple = (0, 1, 2)

{pulserver-0.1.0 → pulserver-0.1.2}/src/pulserver.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pulserver
-Version: 0.1.0
+Version: 0.1.2
 Summary: A PyPulseq-based client/server MR sequence design toolbox.
 Author-email: Matteo Cencini <matteo.cencini@gmail.com>
 Project-URL: Homepage, https://github.com/INFN-MRI/pulserver
@@ -16,6 +16,7 @@ Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.10
 Description-Content-Type: text/x-rst
 License-File: LICENSE.txt
+Requires-Dist: pyyaml
 Requires-Dist: numpy<2.0
 Requires-Dist: scipy<1.14
 Requires-Dist: numba
@@ -39,9 +40,34 @@ Requires-Dist: pydata-sphinx-theme; extra == "doc"
 Requires-Dist: myst-nb; extra == "doc"
 Requires-Dist: matplotlib; extra == "doc"
 Requires-Dist: mrtwin; extra == "doc"
+Requires-Dist: sphinx-copybutton; extra == "doc"
 
 Pulserver
 =========
+|Coverage| |CI/CD| |License| |Codefactor| |Sphinx| |PyPi| |Black| |PythonVersion|
+
+.. |Coverage| image:: https://codecov.io/gh/INFN-MRI/pulserver/graph/badge.svg?token=qtB53xANwI 
+ :target: https://codecov.io/gh/INFN-MRI/pulserver
+
+.. |CI/CD| image:: https://github.com/INFN-MRI/pulserver/workflows/CI-CD/badge.svg
+   :target: https://github.com/INFN-MRI/pulserver
+
+.. |License| image:: https://img.shields.io/github/license/INFN-MRI/pulserver
+   :target: https://github.com/INFN-MRI/pulserver/blob/main/LICENSE.txt
+
+.. |Codefactor| image:: https://www.codefactor.io/repository/github/INFN-MRI/pulserver/badge
+   :target: https://www.codefactor.io/repository/github/INFN-MRI/pulserver
+
+.. |Sphinx| image:: https://img.shields.io/badge/docs-Sphinx-blue
+   :target: https://infn-mri.github.io/pulserver
+
+.. |PyPi| image:: https://img.shields.io/pypi/v/pulserver
+   :target: https://pypi.org/project/pulserver
+
+.. |Black| image:: https://img.shields.io/badge/style-black-black
+
+.. |PythonVersion| image:: https://img.shields.io/badge/Python-%3E=3.10-blue?logo=python&logoColor=white
+   :target: https://python.org
 
 Pulserver is a high-level wrapper over PyPulseq. It is designed to 
 improve MR sequence code organization and provide a bridge

{pulserver-0.1.0 → pulserver-0.1.2}/src/pulserver.egg-info/SOURCES.txt

@@ -3,9 +3,12 @@ LICENSE.txt
 README.rst
 pyproject.toml
 setup.py
+.github/workflows/docker.yml
 .github/workflows/style.yml
 .github/workflows/tags-release.yml
-.github/workflows/test-cicd.yml
+.github/workflows/test-ci.yml
+docker/Dockerfile
+docker/install_pulserver.sh
 docs/Makefile
 docs/api.rst
 docs/client_server_architecture
@@ -33,6 +36,7 @@ src/pulserver/_version.py
 src/pulserver.egg-info/PKG-INFO
 src/pulserver.egg-info/SOURCES.txt
 src/pulserver.egg-info/dependency_links.txt
+src/pulserver.egg-info/entry_points.txt
 src/pulserver.egg-info/requires.txt
 src/pulserver.egg-info/top_level.txt
 src/pulserver/_apps/SPGR2D.py

pulserver-0.1.2/src/pulserver.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+pulserver = pulserver._cli:cli

{pulserver-0.1.0 → pulserver-0.1.2}/src/pulserver.egg-info/requires.txt

@@ -1,3 +1,4 @@
+pyyaml
 numpy<2.0
 scipy<1.14
 numba
@@ -17,6 +18,7 @@ pydata-sphinx-theme
 myst-nb
 matplotlib
 mrtwin
+sphinx-copybutton
 
 [test]
 pytest

pulserver-0.1.0/README.rst

@@ -1,53 +0,0 @@
-Pulserver
-=========
-
-Pulserver is a high-level wrapper over PyPulseq. It is designed to 
-improve MR sequence code organization and provide a bridge
-between different Pulseq interpreter representations while providing
-a familiar interface to PyPulseq user.
-
-It also provide a server-based interface to enable online sequence design
-routines, e.g., using the MR scanner as a client.
-
-Features
---------
-
-
-
-Installation
-------------
-Pulserver can be installed via pip:
-
-.. code-block:: bash
-
-    pip install pulserver
-
-Development
------------
-If you want to modifiy the Pulserver code base:
-
-.. code-block:: bash
-
-    git clone https://github.com/INFN-MRI/pulservert.git
-    pip install -e ./pulserver
-
-Usage
------
-
-TODO: add quick example
-
-Testing
--------
-To run the tests, execute the following command in the terminal:
-
-.. code-block:: bash
-
-     pytest .
-
-License
--------
-This project is licensed under the MIT License.
-
-Contributing
-------------
-Contributions are welcome! Please fork the repository and submit a pull request.