include doc

.gitlab-ci.yml

+before_script:
+  - |
+    docker build --build-arg CACHE_BUSTER=$(openssl rand -hex 12) --build-arg USER=${CI_REGISTRY_USER} --build-arg PASS=${CI_JOB_TOKEN} -t hwmd -f - . <<EOF
+    FROM debian:latest
+    ENV DEBIAN_FRONTEND=noninteractive
+    RUN apt-get update
+    RUN apt-get install -y bash git gcc-12 openmpi-bin libopenmpi-dev build-essential python3 pip indent
+    RUN rm /usr/lib/python*/EXTERNALLY-MANAGED
+    RUN pip install -U autopep8 Jinja2 numpy PyYAML libclang
+    ENV HW_FLAGS="-Wl,--no-as-needed"
+    ENV MPIRUN='mpirun --allow-run-as-root -n 2'
+    ENV OMP_NUM_THREADS=2
+    ARG USER
+    ARG PASS
+    RUN git config --global url."https://\${USER}:\${PASS}@www.ict.inaf.it/gitlab".insteadOf ssh://git@git.ia2.inaf.it
+    WORKDIR /app
+    COPY . /app
+    EOF
+  
+testing:
+  script:
+    - docker run hwmd bash -c './test_install_octree.bash; ./test_checkup.bash; ./test_pip_all.bash; ./test_editable.bash; ./test_bulk.bash' 
\ No newline at end of file

install_and_test.md

@@ -9,7 +9,7 @@ For the user that is not going to edit the code and is only interested in runnin
 For instance, to perform a simulation with particle mesh one can execute:
 
 ```bash
-pip install 'hotwheels_PM[tested] @ git+ssh://git@git.ia2.inaf.it/hotwheels/PM.git@v0.0.0alpha'
+::include{file=test_install_octree.bash}
 ```
 
 This will install also the following hotwheels packages: core, io, timestep. 
@@ -20,7 +20,7 @@ The `[tested]` tag will install the versions of the dependencies used to test th
 To run the C and python tests of the installed `hotwheels` components, run: 
 
 ```bash
-python -m hotwheels.checkup hotwheels
+::include{file=test_checkup.bash}
 ```
 
 Here below some relevant environment variables to change hotwheels default settings:
@@ -46,10 +46,7 @@ Here below some relevant environment variables to change hotwheels default setti
 In case you want to run the module with other `hotwheel` component version you can install each manually:
 
 ```bash
-pip install git+ssh://git@git.ia2.inaf.it/hotwheels/core.git@v0.0.0alpha
-pip install git+ssh://git@git.ia2.inaf.it/hotwheels/io.git@v0.0.0alpha
-pip install git+ssh://git@git.ia2.inaf.it/hotwheels/timestep.git@v0.0.0alpha
-pip install git+ssh://git@git.ia2.inaf.it/hotwheels/PM.git@v0.0.0alpha
+::include{file=test_pip_all.bash}
 ```
 
 ## If you need to put hands on the source code
@@ -58,14 +55,7 @@ In case you find that you need to edit the source code of hotwheels (maybe you f
 can re-install a python module in **editable mode (use -e in pip install)**. For instance, let's suppose that now you need to edit the timestep module and re-run all tests. You can do the following 
 
 ```bash
-git clone ssh://git@git.ia2.inaf.it/hotwheels/timestep.git
-cd timestep
-# very IMPORTANT the -e will install in editable mode
-pip install -e . 
-#
-# edit the files of your choice. Edits will take effect
-# without the need of re-installing the package
-#
+::include{file=test_editable.bash}
 ```
 
 ## Bulk install of all modules
@@ -73,11 +63,11 @@ pip install -e .
 In case you need to work on many modules, you can clone and install all default packages with the [cloneall.bash](cloneall.bash) script:
 
 ```bash
-wget https://www.ict.inaf.it/gitlab/hotwheels/gitlab-profile/-/raw/main/cloneall.bash
-bash cloneall.bash -c # will clone all hotwheels modules
+::include{file=test_editable.bash}
 ```
 
-If you want to create a folder with all the modules soft-linked into the folder `hotwheels/*`, add the flag `-l` to `cloneall.bash` to get this folder tree in a folder named `full/hotwheels/*`. This is helpful in navigating the files with the IDE when development has strong refactoring and one need to edit multiple modules.
+If you want to create a folder with all the modules soft-linked into the folder `hotwheels/*`, add the flag `-l` to `cloneall.bash` to get this folder tree in a folder named `full/hotwheels/*`.
+This is helpful in navigating the files with the IDE when development has strong refactoring and one need to edit multiple modules.
 
 If you want to also create a multi-windows tmux session where each panel corresponds to a hotwheels module add the flag `-t` to `cloneall.bash` (will laso include the folder `full` if exists).
 

test_bulk.bash

+wget https://www.ict.inaf.it/gitlab/hotwheels/gitlab-profile/-/raw/main/cloneall.bash
+bash cloneall.bash -c # will clone all hotwheels modules

test_checkup.bash

+python3 -m hotwheels_core.checkup hotwheels_io

test_editable.bash

+git clone ssh://git@git.ia2.inaf.it/hotwheels/timestep.git
+cd timestep
+# very IMPORTANT the -e will install in editable mode
+pip install -e . 
+#
+# edit the files of your choice. Edits will take effect
+# without the need of re-installing the package
+#

test_install_octree.bash

+pip install 'hotwheels_io[tested] @ git+ssh://git@git.ia2.inaf.it/hotwheels/io.git@v0.0.2alpha'
+

test_pip_all.bash

+pip install git+ssh://git@git.ia2.inaf.it/hotwheels/core.git@v0.0.2alpha
+pip install git+ssh://git@git.ia2.inaf.it/hotwheels/io.git@v0.0.2alpha
+pip install git+ssh://git@git.ia2.inaf.it/hotwheels/timestep.git@v0.0.2alpha
+pip install git+ssh://git@git.ia2.inaf.it/hotwheels/octree.git@v0.0.2alpha
+pip install git+ssh://git@git.ia2.inaf.it/hotwheels/domain.git@v0.0.2alpha
+pip install git+ssh://git@git.ia2.inaf.it/hotwheels/PM.git@v0.0.2alpha
+