Merge branch 'release/0.1.1'

Dockerfile

@@ -0,0 +1,41 @@
+# NOTA BENE
+# YOU SHOULD RUN THIS CONTAINER WITH THE --init OPTION
+
+# STEP 1 - Base image
+FROM ubuntu:18.04
+
+# STEP 2 & 3 - Environment variables needed by miniconda install
+ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
+ENV PATH /opt/conda/bin:$PATH
+
+# STEP 4 - Update Ubuntu and install necessary packages
+RUN apt-get -qq update --fix-missing > /dev/null && \
+    apt-get -qq install -y wget \
+    bzip2 \
+    ca-certificates \
+    curl \
+    git \
+    build-essential  > /dev/null && \
+    apt-get clean > /dev/null && \
+    rm -rf /var/lib/apt/lists/*
+
+# STEP 5 - Install miniconda3
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-4.7.12.1-Linux-x86_64.sh -O ~/miniconda.sh && \
+    /bin/bash ~/miniconda.sh -b -p /opt/conda >/dev/null && \
+    rm ~/miniconda.sh && \
+    /opt/conda/bin/conda clean --all --quiet --yes && \
+    ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
+    /opt/conda/bin/conda update -n base -c defaults conda --yes --quiet > /dev/null && \
+    echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate PHD" >> ~/.bashrc
+
+# STEP 6 - Get a copy of this package
+# RUN git clone https://github.com/fsoubelet/PyhDToolkit /pyhdtoolkit
+COPY . /pyhdtoolkit
+
+# STEP 7 - Create the PHD conda environment
+RUN conda env create --file /pyhdtoolkit/docker_conda_env.yml --force  > /dev/null && \
+    /opt/conda/bin/conda clean --all --quiet --yes > /dev/null
+
+# STEP 8 - Start a bash shell at runtime
+CMD [ "/bin/bash" ]

Makefile

@@ -13,23 +13,25 @@ E = \033[0m
 P = \033[95m
 R = \033[31m
 
-.PHONY : help archive black checklist clean condaenv install isort lines pipreq uninstall tests
+.PHONY : help archive black checklist clean condaenv docker-build docker-pull install isort lines pipreq uninstall tests
 
 all: install
 
 help:
 	@echo "Please use 'make $(R)<target>$(E)' where $(R)<target>$(E) is one of:"
-	@echo "  $(R) archive $(E)      to create a tarball of this specific release."
-	@echo "  $(R) black $(E)        to recursively apply PEP8 formatting through the 'Black' cli tool."
-	@echo "  $(R) checklist $(E)    to print a pre-release check-list."
-	@echo "  $(R) clean $(E)        to recursively remove build, run, and bitecode files/dirs."
-	@echo "  $(R) condaenv $(E)     to 'conda install' the specific 'PHD' environment I use. Personnal."
-	@echo "  $(R) install $(E)      to 'pip install' this package into your activated environment."
-	@echo "  $(R) isort $(E)        to recursively sort import statements. Called by 'make black'."
-	@echo "  $(R) lines $(E)        to count lines of code with the 'tokei' tool."
-	@echo "  $(R) pipreq $(E)       to 'pip install' packages listed in 'requirements.txt' into your activated environment."
-	@echo "  $(R) uninstall $(E)    to uninstall the 'pyhdtoolkit' package from your activated environment."
-	@echo "  $(R) tests $(E)        to run tests with the the pytest package."
+	@echo "  $(R) archive $(E)        to create a tarball of this specific release."
+	@echo "  $(R) black $(E)          to recursively apply PEP8 formatting through the 'Black' cli tool."
+	@echo "  $(R) checklist $(E)      to print a pre-release check-list."
+	@echo "  $(R) clean $(E)          to recursively remove build, run, and bitecode files/dirs."
+	@echo "  $(R) condaenv $(E)       to 'conda install' the specific 'PHD' environment I use. Personnal."
+	@echo "  $(R) docker-build $(E)   to build a container image replicating the 'PHD' environment."
+	@echo "  $(R) docker-pull $(E)    to pull a pre-built image from Dockerhub."
+	@echo "  $(R) install $(E)        to 'pip install' this package into your activated environment."
+	@echo "  $(R) isort $(E)          to recursively sort import statements. Called by 'make black'."
+	@echo "  $(R) lines $(E)          to count lines of code with the 'tokei' tool."
+	@echo "  $(R) pipreq $(E)         to 'pip install' packages listed in 'requirements.txt' into your activated environment."
+	@echo "  $(R) uninstall $(E)      to uninstall the 'pyhdtoolkit' package from your activated environment."
+	@echo "  $(R) tests $(E)          to run tests with the the pytest package."
 
 archive:
 	@echo "$(B)Creating tarball archive of this release.$(E)"
@@ -74,6 +76,15 @@ condaenv:
 	@ipython kernel install --user --name=PHD
 	@conda deactivate
 
+docker-build:
+	@echo "Building docker image with $(D)PHD$(E) conda environment, with tag $(P)simenv$(E)."
+	@docker build -t simenv .
+	@echo "Done. You can run this with $(P)docker run -it --init simenv$(E)."
+
+docker-pull:
+	@echo "Pulling docker image $(P)fsoubelet/simenv$(E) from Dockerhub."
+	@docker pull fsoubelet/simenv
+
 install: black clean
 	@echo "Installing this package to your active environment."
 	@pip install .

README.md

@@ -5,18 +5,19 @@ This repository is a package gathering a number of Python utilities for my work.
 ## Installation
 
 This code is compatible with `Python 3.6+`.
-If for some reason you have a need for this package, first install the prerequisites with:
+If for some reason you have a need for it, you should first install the prerequisites with:
 ```bash
 make pipreq
 ```
 
 Then, you can simply install it with:
 ```bash
-pip install -e git+https://github.com/fsoubelet/PyhDToolkit.git@master#egg=pyhdtoolkit
+pip install --editable git+https://github.com/fsoubelet/PyhDToolkit.git@master#egg=pyhdtoolkit
 ```
 
-The `-e` flag should only be included if you intend to make some hotfix changes to the site-package.
-If you intend on making actual changes, then you should clone this repository through VCS, and install it into your virtual environment with:
+The `--editable` flag should only be included if you intend to make some hotfix changes to the site-package.
+If you intend on making actual changes, then you should clone this repository through VCS, and install it into a virtual environment.
+With `git`, this would be:
 ```bash
 git clone https://github.com/fsoubelet/PyhDToolkit.git
 cd PyhDToolkit
@@ -35,8 +36,7 @@ make tests
 
 ## Standards, Tools and VCS
 
-This repository respects the PyCharm docstring format, and uses [Black][black_formatter] as a code formatter.
-The default enforced line length is 120 characters.
+This repository respects the PyCharm docstring format, and uses [Black][black_formatter] as a code formatter with a default enforced line length of 120 characters.
 You can lint the code with:
 ```bash
 make black
@@ -45,21 +45,49 @@ make black
 VCS is done through [git][git_ref] and follows the [Gitflow][gitflow_ref] workflow.
 As a consequence, make sure to always install from `master`.
 
-## Miscellaneous Goodies
+## Miscellaneous
 
 Feel free to explore the `Makefile` and make use of the functions it offers.
-You can get an idea of what is available to you by running:
+You will get an idea of what functionality is available to you by running:
 ```bash
 make help
 ```
 
+### Environment 
+
 This repository currently comes with an `environment.yml` file to reproduce a fully compatible conda environment.
 You can install this environment and add it to your ipython kernel by running:
 ```bash
 make condaenv
 ```
 
-A Dockerfile and later on an [OCI][oci_ref]-compliant file are to come.
+### Container
+
+A Dockerfile is included if you want to build a container image from source.
+You can do so, building with the tag `simenv`, with the command:
+```bash
+make docker-build
+```
+
+Alternatively, you can directly pull a pre-built image from Dockerhub with:
+```bash
+make docker-pull
+```
+
+You can then run your container in interactive mode, and use the already activated conda environment for your work.
+It is highly advised to run with `--init` for zombie processes protection, see [Tini][tini_ref] for details.
+Assuming you pulled the provided image from Dockerhub, the command is then:
+```bash
+docker run -it --init fsoubelet/simenv
+```
+
+If you want to do some exploration through a `jupyter` interface then you need to tell your container to install it first, as it is not bundled in miniconda, then add the custom environment kernelspec.
+The following command will take care of all this:
+```bash
+docker run -it --init -p 8888:8888 fsoubelet/simenv /bin/bash -c "/opt/conda/bin/conda install -c conda-forge jupyterlab -y --quiet > /dev/null && mkdir /opt/notebooks && /opt/conda/envs/PHD/bin/ipython kernel install --user --name=PHD && /opt/conda/bin/jupyter lab --notebook-dir=/opt/notebooks --ip='*' --port=8888 --no-browser --allow-root"
+```
+
+You can then copy the provided token and head to `localhost:8888` on your local machine.
 
 ## License
 
@@ -69,4 +97,5 @@ Copyright © 2019-2020 Felix Soubelet. [MIT License][license]
 [gitflow_ref]: https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow
 [git_ref]: https://git-scm.com/
 [license]: https://github.com/fsoubelet/PyhDToolkit/blob/master/LICENSE
-[oci_ref]: https://www.opencontainers.org/
+[oci_ref]: https://www.opencontainers.org/
+[tini_ref]: https://github.com/krallin/tini

docker_conda_env.yml

@@ -0,0 +1,110 @@
+name: PHD
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - alabaster=0.7.12
+  - attrs=19.3.0
+  - babel=2.7.0
+  - backcall=0.1.0
+  - bleach=3.1.0
+  - bzip2=1.0.8
+  - ca-certificates=2019.11.28
+  - certifi=2019.11.28
+  - cffi=1.13.2
+  - chardet=3.0.4
+  - cmarkgfm=0.4.2
+  - cryptography=2.8
+  - cycler=0.10.0
+  - decorator=4.4.1
+  - docutils=0.15.2
+  - freetype=2.10.0
+  - future=0.18.2
+  - h5py=2.10.0
+  - hdf5=1.10.5
+  - idna=2.8
+  - imagesize=1.1.0
+  - importlib_metadata=1.3.0
+  - ipykernel=5.1.3
+  - ipython=7.10.2
+  - ipython_genutils=0.2.0
+  - jedi=0.15.1
+  - jinja2=2.10.3
+  - joblib=0.14.1
+  - jpype1=0.7
+  - jupyter_client=5.3.3
+  - jupyter_core=4.6.1
+  - kiwisolver=1.1.0
+  - libblas=3.8.0
+  - libcblas=3.8.0
+  - libcxx=9.0.0
+  - libffi=3.2.1
+  - liblapack=3.8.0
+  - libopenblas=0.3.7
+  - libpng=1.6.37
+  - libsodium=1.0.17
+  - llvm-openmp=9.0.0
+  - markupsafe=1.1.1
+  - matplotlib=3.1.2
+  - matplotlib-base=3.1.2
+  - more-itertools=8.0.2
+  - ncurses=6.1
+  - numpy=1.17.3
+  - openssl=1.1.1d
+  - packaging=19.2
+  - pandas=0.25.3
+  - parso=0.5.2
+  - pexpect=4.7.0
+  - pickleshare=0.7.5
+  - pip=19.3.1
+  - pkginfo=1.5.0.1
+  - pluggy=0.12.0
+  - prompt_toolkit=3.0.2
+  - ptyprocess=0.6.0
+  - py=1.8.0
+  - pycparser=2.19
+  - pygments=2.5.2
+  - pyopenssl=19.1.0
+  - pyparsing=2.4.5
+  - pysocks=1.7.1
+  - pytest=5.3.2
+  - python=3.7.3
+  - python-dateutil=2.8.1
+  - pytz=2019.3
+  - pyzmq=18.1.1
+  - readline=8.0
+  - readme_renderer=24.0
+  - requests=2.22.0
+  - requests-toolbelt=0.9.1
+  - scikit-learn=0.22
+  - scipy=1.3.2
+  - setuptools=42.0.2
+  - six=1.13.0
+  - snowballstemmer=2.0.0
+  - sphinx=2.3.0
+  - sphinxcontrib-applehelp=1.0.1
+  - sphinxcontrib-devhelp=1.0.1
+  - sphinxcontrib-htmlhelp=1.0.2
+  - sphinxcontrib-jsmath=1.0.1
+  - sphinxcontrib-qthelp=1.0.2
+  - sphinxcontrib-serializinghtml=1.1.3
+  - sqlite=3.30.1
+  - tk=8.6.10
+  - tornado=6.0.3
+  - tqdm=4.40.2
+  - traitlets=4.3.3
+  - twine=2.0.0
+  - urllib3=1.25.7
+  - wcwidth=0.1.7
+  - webencodings=0.5.1
+  - wheel=0.33.6
+  - xz=5.2.4
+  - zeromq=4.3.2
+  - zipp=0.6.0
+  - zlib=1.2.11
+  - pip:
+    - cmmnbuild-dep-manager==2.2.5
+    - pytimber==2.7.0
+    - sdds==0.1.3
+    - tfs-pandas==1.0.3
+    - cpymad==1.4.1

pyhdtoolkit/__version__.py

@@ -1,7 +1,7 @@
 __title__ = "pyhdtoolkit"
 __description__ = "An all-in-one toolkit package to easy my Python work in my PhD."
 __url__ = "https://github.com/fsoubelet/PyhDToolkit"
-__version__ = "0.1.0"
+__version__ = "0.1.1"
 __author__ = "Felix Soubelet"
 __author_email__ = "felix.soubelet@cern.ch"
 __license__ = "MIT"

requirements.txt

@@ -2,4 +2,6 @@ tqdm
 pandas
 pytest
 matplotlib
-numpy
+numpy
+pandas
+scipy