From ec42373df6921fe671a87c0b00da1aad71e42d85 Mon Sep 17 00:00:00 2001
From: Amir MOHAMMADI <amir.mohammadi@idiap.ch>
Date: Fri, 13 May 2022 15:15:41 +0200
Subject: [PATCH] update docs for mamba and bob-devel
---
bob/devtools/data/conda_build_config.yaml | 45 -----------------------
conda/meta.yaml | 1 +
doc/development.rst | 6 +--
doc/install.rst | 16 +++++---
doc/links.rst | 2 +
doc/templates.rst | 38 +++++--------------
6 files changed, 26 insertions(+), 82 deletions(-)
diff --git a/bob/devtools/data/conda_build_config.yaml b/bob/devtools/data/conda_build_config.yaml
index ca99d2c7..7c1b96ae 100644
--- a/bob/devtools/data/conda_build_config.yaml
+++ b/bob/devtools/data/conda_build_config.yaml
@@ -341,8 +341,6 @@ package_names_map:
pytorch_lightning: pytorch-lightning
-boost:
- - 1.77.0
click:
- 8.0.4
click_plugins:
@@ -365,45 +363,24 @@ docker_py:
- 5.0.3
docopt:
- 0.6.2
-ffmpeg:
- - 4.3.2
flaky:
- 3.7.0
font_ttf_dejavu_sans_mono:
- 2.37
freetype:
- 2.10.4
-giflib:
- - 5.2.1
graphviz:
- 2.50.0
h5py:
- 3.6.0
-hdf5:
- - 1.12.1
imageio:
- 2.16.1
imageio_ffmpeg:
- 0.4.5
-jinja2:
- - 3.0.3
-jpeg:
- - 9e
-jsonschema:
- - 4.4.0
-libblitz:
- - 1.0.2
-libpng:
- - 1.6.37
-libtiff:
- - 4.3.0
make:
- 4.3
matplotlib:
- 3.5.1
-mkl: # [x86 or x86_64]
- - 2022.0.1 # [linux and (x86 or x86_64)]
- - 2022.0.0 # [osx and (x86 or x86_64)]
ncurses:
- 6.3
nose:
@@ -424,18 +401,8 @@ pkg_config:
- 0.29.2
psutil:
- 5.9.0
-psycopg2:
- - 2.9.3
pybind11:
- 2.9.1
-pyopengl:
- - 3.1.6
-pyqt: # [not arm64]
- - 5.12.3 # [not arm64]
-pyqtgraph:
- - 0.12.3
-pytables:
- - 3.7.0
pytest:
- 7.0.1
pytest_cov:
@@ -447,14 +414,8 @@ pytorch:
- 1.10.2 # [osx]
pytorch_lightning:
- 1.6.0
-pyyaml:
- - 6.0
pyzmq:
- 22.3.0
-qdarkstyle:
- - 3.0.3
-qtpy:
- - 2.0.1
requests:
- 2.27.1
schema:
@@ -471,16 +432,10 @@ simplejson:
- 3.17.6
six:
- 1.16.0
-sox:
- - 14.4.2
sphinx:
- 4.4.0
sphinx_rtd_theme:
- 1.0.0
-sphinxcontrib_httpdomain:
- - 1.8.0
-sphinxcontrib_mermaid:
- - 0.7.1
sphinxcontrib_programoutput:
- 0.16
sqlalchemy:
diff --git a/conda/meta.yaml b/conda/meta.yaml
index fbcf008c..cbeef839 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -54,6 +54,7 @@ requirements:
- python-graphviz
- pip
- webdavclient3
+ - pre-commit
test:
requires:
diff --git a/doc/development.rst b/doc/development.rst
index a66a3f11..9dfb237c 100644
--- a/doc/development.rst
+++ b/doc/development.rst
@@ -194,11 +194,11 @@ You can see what is installed in your environment:
$ conda list
-And you can install new packages using conda:
+And you can install new packages using mamba:
.. code-block:: sh
- $ conda install <package>
+ $ mamba install <package>
.. note::
@@ -290,7 +290,7 @@ your environment. You can find these dependencies by checking
.. code-block:: sh
- $ conda install gcc_linux-64 gxx_linux-64 libblitz
+ $ mamba install gcc_linux-64 gxx_linux-64 libblitz
$ bdt dev install src/bob.extension src/bob.io.base # the order of installing dependencies matters!
.. include:: links.rst
diff --git a/doc/install.rst b/doc/install.rst
index 46d56803..e6aec990 100644
--- a/doc/install.rst
+++ b/doc/install.rst
@@ -7,16 +7,16 @@
Installation
==============
-You can install this package via conda_, simply pointing to our beta channel.
+You can install this package via conda_ or mamba_, simply pointing to our beta channel.
We provide packages for both 64-bit Linux and MacOS, for Python 3.8+.
.. code-block:: sh
- $ conda install -n base -c https://www.idiap.ch/software/bob/conda/label/beta -c conda-forge bob.devtools
+ $ mamba install -n base -c https://www.idiap.ch/software/bob/conda/label/beta -c conda-forge bob.devtools
.. warning::
- Some commands from this package will use the ``conda`` CLI to install
+ Some commands from this package will use the ``mamba`` CLI to install
packages on new environments.
If you install bob.devtools on another environment which is not ``base``, a
@@ -24,17 +24,23 @@ We provide packages for both 64-bit Linux and MacOS, for Python 3.8+.
duplicating the size of your conda installation. For this reason, we
recommend you install this package on the ``base`` environment.
-You must also create an alias for ``bdt`` because some commands require another
-conda environment to be activated:
+Installing bob.devtools will create a terminal command called ``bdt`` which you
+must create an alias for it because some ``bdt`` commands require another conda
+environment to be activated. Moreover, development of Bob packages depend on
+pre-commit_ (pre-commit gets installed as a dependency of bob.devtools) so you
+will need an alias for that as well:
.. code-block:: sh
$ conda activate base
$ echo "alias bdt=$(which bdt)" >> ~/.bashrc
+ # you will also need pre-commit which gets installed when you install bob.devtools
+ $ echo "alias pre-commit=$(which pre-commit)" >> ~/.bashrc
$ source ~/.bashrc
# test if it works
$ conda deactivate
$ bdt --help
+ $ pre-commit --help
.. _bob.devtools.install.setup:
diff --git a/doc/links.rst b/doc/links.rst
index 6a5cb7f2..53387a73 100644
--- a/doc/links.rst
+++ b/doc/links.rst
@@ -3,6 +3,8 @@
.. Place here references to all citations in lower case
.. _conda: https://conda.io
+.. _mamba: https://mamba.readthedocs.io/
+.. _pre-commit: https://pre-commit.com/
.. _bob: https://www.idiap.ch/software/bob
.. _beat: https://www.idiap.ch/software/beat
.. _shell executor: https://docs.gitlab.com/runner/executors/shell.html
diff --git a/doc/templates.rst b/doc/templates.rst
index 089591ab..2e5b159a 100644
--- a/doc/templates.rst
+++ b/doc/templates.rst
@@ -434,11 +434,6 @@ you should perform some extra steps:
python_graphviz: python-graphviz
scikit_image: scikit-image
scikit_learn: scikit-learn
- sphinxcontrib_httpdomain: sphinxcontrib-httpdomain
- sphinxcontrib_mermaid: sphinxcontrib-mermaid
- sphinxcontrib_programoutput: sphinxcontrib-programoutput
- zc_buildout: zc.buildout
- zc_recipe_egg: zc.recipe.egg
boost:
@@ -464,36 +459,21 @@ Updating a dependency version
All dependencies versions are listed in
``bob/bob.devtools/bob/devtools/data/conda_build_config.yaml`` to ensure that
-all bob packages use compatible versions of those dependencies. When updating
-(or adding a new) dependency, you must make sure that the new version doesn't
-conflicts with **all** other dependencies. Often, a newest verion of your
-dependency has newer requirements for its own dependencies, which can conflict
-with the rest of ``bob`` dependencies. Therefore it is often best to update all
-dependencies at once, not just one. To do so, ask ``conda`` to create an
-environment with all ``bob`` dependencies:
+all bob packages use compatible versions of those dependencies. This file cannot
+be modified by hand and there is no way to update just one dependency. A script
+is provided to update dependency versions and you have to use that:
.. code-block:: bash
- conda create -n bob_deps --dry-run --override-channels --strict-channel-priority \\
- -c http://www.idiap.ch/software/bob/conda \\
- -c conda-forge \\
- python=3.8 \\ # fix the python version
- click-plugins cmake coverage dask ... [all bob dependencies]
-
-The versions solved by ``conda`` should be the newest compatible ones you can
-use. If you require a specific version of a dependency, say ``h5py`` you can
-specify only that version in the ``conda`` command and let conda solve the
-rest. Note that you have to update the pinned version of all packages at once
-according to the ``conda create`` output. It is not possible to just update
-the version of one dependency alone.
+ $ git clone git@gitlab.idiap.ch:bob/bob.devtools.git
+ $ cd bob.devtools
+ $ python bob/devtools/scripts/update_pins.py --help
.. note::
- '.' or '-' in package names are changed to '_' in the
- ``conda_build_config.yaml`` file. Make sure to use the real packages name in
- the ``conda`` command. Moreover, please remember to update the
- ``package_names_map`` field if you add a new dependecy with `.` or `-` in its
- name.
+ If you are adding a new package and it has '.' or '-' in its pacakge name, you
+ must list it in the ``package_names_map`` block of the
+ ``conda_build_config.yaml`` file.
Conda recipe
--
GitLab