Merge branch 'main' into ess-main

.github/workflows/compilation.yml

@@ -0,0 +1,123 @@
+name: build-pyorbit
+
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    tags:
+      - '*'
+    branches:
+      - '*'
+
+jobs:
+
+
+  apple-silicon:
+    runs-on: macos-14
+    steps:
+      - name: Install packages
+        run: |
+          brew reinstall pkg-config fftw
+
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Build
+        run: |
+          .github/workflows/pip-build.sh
+
+      - name: Test
+        run: |
+          .github/workflows/pip-tests.sh
+
+      - name: Print Versions
+        run: |
+          .github/workflows/pip-versions.sh
+
+
+  centos-stream:
+    runs-on: ubuntu-latest
+    container:
+      image: quay.io/centos/centos:stream9
+    steps:
+         - name: Install packages
+           run: |
+             dnf group install -y "Development Tools"
+             dnf install -y python3-devel fftw3-devel
+
+         - uses: actions/checkout@v4
+           with:
+            fetch-depth: 0
+         - name: Build
+           run: |
+             .github/workflows/pip-build.sh
+
+         - name: Test
+           run: |
+             .github/workflows/pip-tests.sh
+
+         - name: Print Versions
+           run: |
+             .github/workflows/pip-versions.sh
+
+
+
+  ubuntu:
+    runs-on: ubuntu-latest
+    container:
+      image: ubuntu:latest
+    steps:
+         - name: Install packages
+           run: |
+             apt-get update -y
+             apt-get install -y  build-essential python3 libfftw3-dev python3-venv libpython3-dev pkg-config git
+
+         - uses: actions/checkout@v4
+           with:
+            fetch-depth: 0
+
+         - name: Build
+           run: |
+             .github/workflows/pip-build.sh
+
+         - name: Test
+           run: |
+             .github/workflows/pip-tests.sh
+
+         - name: Print Versions
+           run: |
+             .github/workflows/pip-versions.sh
+
+
+  conda:
+    runs-on: ubuntu-latest
+    container:
+      image: ubuntu:latest
+    steps:
+         - name: Install Conda
+           run: |
+             apt update -y
+             apt install -y curl gpg git build-essential
+             curl https://repo.anaconda.com/pkgs/misc/gpgkeys/anaconda.asc | gpg --dearmor > conda.gpg
+             install -o root -g root -m 644 conda.gpg /usr/share/keyrings/conda-archive-keyring.gpg
+             echo "deb [arch=amd64 signed-by=/usr/share/keyrings/conda-archive-keyring.gpg] https://repo.anaconda.com/pkgs/misc/debrepo/conda stable main" > /etc/apt/sources.list.d/conda.list
+             apt update -y
+             apt install -y conda
+
+         - uses: actions/checkout@v4
+           with:
+            fetch-depth: 0
+
+         - name: Build
+           run: |
+             .github/workflows/conda-build.sh
+
+         - name: Test
+           run: |
+             .github/workflows/conda-tests.sh
+
+         - name: Print Versions
+           run: |
+             .github/workflows/conda-versions.sh

.github/workflows/conda-build.sh

@@ -0,0 +1,5 @@
+. /opt/conda/etc/profile.d/conda.sh
+conda env create -n po3 --file environment.yml
+conda activate po3
+pip install -U meson-python setuptools setuptools-scm
+pip install --no-build-isolation --editable .

.github/workflows/conda-tests.sh

@@ -0,0 +1,4 @@
+. /opt/conda/etc/profile.d/conda.sh
+conda activate po3
+cd examples/SNS_Linac/pyorbit3_linac_model/
+python pyorbit3_sns_linac_mebt_hebt2.py

.github/workflows/conda-versions.sh

@@ -0,0 +1,7 @@
+. /opt/conda/etc/profile.d/conda.sh
+conda activate po3
+python -V
+conda -V
+pip -V
+gcc -v
+python -m setuptools_scm

.github/workflows/pip-build.sh

@@ -0,0 +1,6 @@
+python3 -m venv .po3
+. .po3/bin/activate
+pip install -U pip
+pip install -r requirements.txt
+pip install -U setuptools
+pip install --no-build-isolation --editable .

.github/workflows/pip-tests.sh

@@ -0,0 +1,3 @@
+. .po3/bin/activate
+cd examples/SNS_Linac/pyorbit3_linac_model/
+python pyorbit3_sns_linac_mebt_hebt2.py

.github/workflows/pip-versions.sh

@@ -0,0 +1,5 @@
+. .po3/bin/activate
+python -V
+pip -V
+gcc -v
+python -m setuptools_scm

.gitlab-ci.yml

@@ -1,4 +1,3 @@
-
 include:
   - remote: "https://gitlab.esss.lu.se/ics-infrastructure/gitlab-ci-yml/raw/master/PreCommit.gitlab-ci.yml"
   - remote: "https://gitlab.esss.lu.se/ics-infrastructure/gitlab-ci-yml/raw/master/ArtifactoryPyPI.gitlab-ci.yml"
@@ -12,10 +11,13 @@ run-tests:
   tags:
     - docker
   stage: test
-  image: continuumio/miniconda3:23.5.2-0
+  image: continuumio/miniconda3:24.7.1-0
   before_script:
-    - conda install -c conda-forge gcc gxx fftw mpich pytest pytest-cov coverage numpy scipy matplotlib
-    - python setup.py clean
+    - conda env create -y -n po3 --file environment.yml
+    - conda init bash
+    - source ~/.bashrc
+    - conda activate po3
+    - conda install -y -c conda-forge gcc gxx mpich mpich-mpicc mpich-mpicxx pytest pytest-cov coverage numpy scipy matplotlib
     - pip install .
   script:
     - pytest tests --junitxml=junit.xml --cov-report xml --cov-report term --cov orbit
@@ -32,23 +34,24 @@ run-tests:
 
 build-pypi-package-py310:
   extends: build-pypi-package
-  image: conda/miniconda3-centos7:latest
+  image: continuumio/miniconda3:24.7.1-0
   before_script:
-    - yum install -y gcc gcc-c++
     - conda update -y -n base -c defaults conda
-    - conda create -y -n python310 python=3.10
+    - conda env create -y -n python310 --file environment.yml
     - conda init bash
     - source ~/.bashrc
     - conda activate python310
-    - conda install -y -c conda-forge git fftw mpich mpich-mpicc mpich-mpicxx
+    - conda install -y -c conda-forge python=3.10 build gcc gxx git mpich mpich-mpicc mpich-mpicxx
 
 build-pypi-package:
-  image: conda/miniconda3-centos7:latest
+  image: continuumio/miniconda3:24.7.1-0
+  script:
+    - git config --global --add safe.directory /builds/ess-crs/pyorbit3
+    - python -m build
   before_script:
-    - yum install -y gcc gcc-c++
     - conda update -y -n base -c defaults conda
-    - conda create -y -n python311 python=3.11
+    - conda env create -y -n python311 --file environment.yml
     - conda init bash
     - source ~/.bashrc
     - conda activate python311
-    - conda install -y -c conda-forge git fftw mpich mpich-mpicc mpich-mpicxx
+    - conda install -y -c conda-forge python=3.11 build gcc gxx git git-lfs mpich mpich-mpicc mpich-mpicxx

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
     hooks:
     - id: end-of-file-fixer
     - id: trailing-whitespace
-      exclude: '^tests/examples/SNS_Linac/linac_errors/.*|^tests/examples/AccLattice_Tests/.*|^tests/examples/Optimization/.*'
+      exclude: '^tests/examples/SNS_Linac/linac_errors/.*|^tests/examples/AccLattice_Tests/.*|^tests/examples/Optimization/.*|^.*\.dat'
 
 
   - repo: https://github.com/ambv/black

MesonBuild.md

@@ -0,0 +1,75 @@
+# PyOrbit3 with meson
+
+This uses meson-python to build orbit package.
+
+There is no **setup.py** file, instead we have **meson.build**.
+**pyproject.toml** is changed to use meson.
+
+This is experimental setup that is work in progress.
+The pure python part is built with hierarchical **meson.build** files in **py/**.
+The C++ setup is combined in one file **src/meson.build**.
+
+### Main modifications in C++ code
+1. **src/libmain/** is not used, still there for reference but will be gone soon.
+2. **src/core/** contains one C++ file per module inside _orbit.core_
+3. The files **wrap_XXXX.cc** were modified to correctly reference modules
+```cpp
+// line
+PyObject* mod = PyImport_ImportModule("_bunch");
+// replaced with
+PyObject* mod = PyImport_ImportModule("orbit.core.bunch");
+```
+
+
+
+# Setup
+
+## 0. Required software
+
+One needs compilers, python and libfftw (and potentially mpi).
+See [PyORBIT3](https://github.com/PyORBIT-Collaboration/PyORBIT3) for external
+requirements.
+
+
+## 1. Preparing environment
+
+First step is to clone the source code from meson branch:
+
+```bash
+git clone -b meson https://github.com/azukov/PyORBIT3.git
+```
+
+Initialize new virtual environment and install packages
+
+```
+python -m venv .mes
+source .mes/bin/activate
+pip install -U pip
+pip install -r requirements
+```
+Edit **meson.build** and set correct paths/flags for python/fftw3 headers and libraries
+
+## 2. Build
+
+To install orbit package in development mode run following:
+```bash
+ pip install --no-build-isolation --editable .
+```
+No rebuild is necessary, just edit **py/** or **src/** and meson will rebuild as needed when import happens.
+
+
+## 3. Run examples
+
+Special examples used for meson testing
+
+```bash
+cd examples/meson
+python imports_test.py
+python uspas_test.py
+```
+
+SNS linac example
+```bash
+cd examples/SNS_Linac/pyorbit3_linac_model/
+python pyorbit3_sns_linac_mebt_hebt2.py
+```