From 47efeab6be03224e6f7bdb259ea4707ddfc1b054 Mon Sep 17 00:00:00 2001
From: Luis Antonio Obis Aparicio <35803280+lobis@users.noreply.github.com>
Date: Tue, 1 Oct 2024 12:32:17 +0200
Subject: [PATCH] Dockerfile to build from source (#66)

* update readme and Dockerfile

* style: pre-commit fixes

* cmake old policy

* move cmake configurable info to top

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .dockerignore  |  1 -
 CMakeLists.txt |  9 +++----
 Dockerfile     | 19 +++++++++++++--
 README.md      | 65 ++++++++++++++++++++++++++++++++++++++++----------
 4 files changed, 75 insertions(+), 19 deletions(-)

diff --git a/.dockerignore b/.dockerignore
index b0e52b8..d9f0d07 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -4,4 +4,3 @@ build
 *_cache
 .github
 tests
-.*
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1c98830..6401d93 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,4 +1,9 @@
 cmake_minimum_required(VERSION 3.25...3.30)
+cmake_policy(SET CMP0169 OLD)
+
+set(CMAKE_CXX_STANDARD 17)
+set(AWKWARD_VERSION "v2.6.8")
+set(PYBIND11_VERSION "v2.13.6")
 
 if (NOT DEFINED SKBUILD_PROJECT_NAME)
     # IDE
@@ -9,13 +14,9 @@ project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX)
 
 set(PYTHON_MODULE_NAME _geant4_application)
 
-set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 
-set(AWKWARD_VERSION "v2.6.8")
-set(PYBIND11_VERSION "v2.13.6")
-
 find_package(
     Python
     COMPONENTS Interpreter Development.Module
diff --git a/Dockerfile b/Dockerfile
index a42cd4c..537ed81 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,5 +1,20 @@
-FROM python:3.12-slim-bullseye as builder
+FROM ubuntu:latest
 
-RUN python -m pip install --no-cache-dir geant4-python-application
+RUN apt-get update && apt-get install -y python3 python3-pip python-is-python3 git cmake build-essential libxerces-c-dev && apt-get clean
+
+ENV Geant4_DIR=/geant4
+
+RUN git clone https://github.com/Geant4/geant4.git /geant4-source --depth 1 --branch v11.2.2 && \
+    cmake -B geant4-build -S geant4-source -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${Geant4_DIR} -DCMAKE_CXX_STANDARD=17 -DGEANT4_USE_GDML=ON  \
+    -DGEANT4_INSTALL_EXAMPLES=OFF -DGEANT4_INSTALL_DATA=OFF -DGEANT4_BUILD_TLS_MODEL=global-dynamic -DBUILD_STATIC_LIBS=ON -DBUILD_SHARED_LIBS=OFF \
+    -DCMAKE_CXX_FLAGS=-fPIC -DCMAKE_C_FLAGS=-fPIC -DGEANT4_USE_SYSTEM_EXPAT=OFF && \
+    cmake --build geant4-build --parallel $(nproc) --config Release --target install && \
+    rm -rf geant4-source geant4-build
+
+COPY . /src
+
+RUN cd /src && pip install . --break-system-packages && cd / && rm -rf /src
+
+WORKDIR /
 
 ENTRYPOINT ["python"]
diff --git a/README.md b/README.md
index 890185f..a9e091f 100644
--- a/README.md
+++ b/README.md
@@ -19,28 +19,69 @@ looking at [geant4_pybind](https://github.com/HaarigerHarald/geant4_pybind).
 - Python interface to the application via
   [pybind11](https://github.com/pybind/pybind11)
 - The complete event data is available as an
-  [awkward array](https://github.com/scikit-hep/awkward) for further analysis
+  [awkward array](https://github.com/scikit-hep/awkward)
 
 ## Installation
 
-A lot of work has been done to make the installation as easy as possible. This
-package is fully pip installable and should work on all major platforms.
+The package is pip installable and should work on all major platforms. Geant4 is
+not required to be installed on the system as the PyPI distribution includes a
+statically linked version of Geant4.
 
-The package itself does not contain any Geant4 data files. These files are
-needed to perform any kind of simulation. They will be downloaded to a temporary
-directory automatically during simulation startup.
+However, for the time being, it's recommended to install from the GitHub
+repository to get the latest version, which makes Geant4 a necessary dependency.
+
+The provided `Dockerfile` can be used for development purposes and as
+documentation on the required dependencies. To build the image run from the root
+directory:
+
+```bash
+docker build -t geant4-python-application .
+```
+
+Geant4 can be installed using conda:
+
+```bash
+conda install -c conda-forge geant4
+```
+
+For development purposes however, it's recommended to install Geant4 from source
+with a similar configuration to the one used in the CI:
+
+```bash
+git clone https://github.com/Geant4/geant4.git ./geant4-source --depth 1 --branch v11.2.2
+
+cmake -B ./geant4-build -S ./geant4-source -DCMAKE_INSTALL_PREFIX=./geant4-install -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_STANDARD=17 -DGEANT4_USE_GDML=ON -DGEANT4_INSTALL_EXAMPLES=OFF -DGEANT4_INSTALL_DATA=OFF -DGEANT4_BUILD_TLS_MODEL=global-dynamic -DBUILD_STATIC_LIBS=ON -DBUILD_SHARED_LIBS=OFF -DCMAKE_CXX_FLAGS=-fPIC -DCMAKE_C_FLAGS=-fPIC -DGEANT4_USE_SYSTEM_EXPAT=OFF
+cmake --build ./geant4-build --parallel $(nproc) --config Release --target install
+```
+
+One common installation issue is the dependency `xerces-c`. You may be able to
+install it from your package manager (e.g. `apt-get install libxerces-c-dev) but
+it's also possible to build it from source. In this case make sure the
+installation directory is accessible or just use the default system path.
+
+```bash
+git clone https://github.com/apache/xerces-c.git ./xerces-source
+git -C ./xerces-source checkout tags/v3.2.5
+cmake -B ./xerces-build -S ./xerces-source -DCMAKE_INSTALL_PREFIX=./xerces-install  -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_STANDARD=17 -DBUILD_SHARED_LIBS=OFF -DCMAKE_CXX_FLAGS=-fPIC -DCMAKE_C_FLAGS=-fPIC -Dnetwork-accessor=socket -Dtranscoder=iconv
+cmake --build ./xerces-build --parallel $(nproc) --config Release --target install
+```
+
+After all dependencies are met, you should be able to install the package by
+running the following command from the root directory:
 
 ```bash
-pip install geant4-python-application
+pip install .
 ```
 
 ### Geant4 data files
 
-The Python wheels for this package do not contain any Geant4 data files due to
-their size. These files will be downloaded on demand without the need of any
-user interaction.
+Geant4 comes with a large set of data files which are required in order to run.
+The data files are the bulk of the Geant4 installation and can be quite large.
+These data files are not included in the Python wheels for this package due to
+its size.
 
-The default location for these files can be obtained by calling:
+The python package automatically manages the download of the data files. To
+check the location of the data files, run the following command:
 
 ```bash
 python -c "import geant4_python_application; print(geant4_python_application.get_data_path())"
@@ -74,7 +115,7 @@ from geant4_python_application import application_directory
 application_directory(temp=True)
 ```
 
-The operating system will take care of cleaning up the temporary directory.
+The operating system should take care of cleaning up the temporary directory.
 
 It is possible that the operating system will delete only some of the files in
 the temporary directory which can lead to a Geant4 runtime error. In this case