Building conda packages

This tutorial describes how to build a conda package

Install Miniconda or Anaconda, conda-build and Git
- After installing miniconda or anaconda, use conda to install conda-build and Git.
- To install conda-build in your terminal window or an anaconda prompt, run:
```
  conda install conda-build
```
- Git can be installed by following the steps mentioned here.
- Follow Building conda packages with conda skeleton. The lab’s GitHub template already has the basic skeleton.

Edit the meta.yaml file. It should look something like this:

 {% set version = "1.1.0" %}

 package:
 name: imagesize
 version: {{ version }}

 source:
 git_url: https://github.com/ilanschnell/bsdiff4.git
 git_rev: 1.1.4
 git_depth: 1 # (Defaults to -1/not shallow)

 build:
 noarch: python
 number: 0
 script: python -m pip install .

 requirements:
 host:
     - python
     - pip
 run:
     - python

 test:
 imports:
     - imagesize

 about:
 home: https://github.com/shibukawa/imagesize_py
 license: MIT
 summary: 'Getting image size from png/jpeg/jpeg2000/gif file'
 description: |
     This module analyzes jpeg/jpeg2000/png/gif image header and
     return image size.
 dev_url: https://github.com/shibukawa/imagesize_py
 doc_url: https://pypi.python.org/pypi/imagesize
 doc_source_url: https://github.com/shibukawa/imagesize_py/blob/master/README.rst

Here is another example from the pyCapsid repository

 #{% set data = load_setup_py_data() %}

 package:
 name: pycapsid
 version: 0.1.9

 source:
 path: ..
 #url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
 # If getting the source from GitHub, remove the line above,
 # uncomment the line below, and modify as needed. Use releases if available:
 #url: https://github.com/luquelab/pyCapsid/archive/refs/heads/colin_branch.zip
 # and otherwise fall back to archive:
 # url: https://github.com/simplejson/simplejson/archive/v{{ version }}.tar.gz
 #sha256: 2b3a0c466fb4a1014ea131c2b8ea7c519f9278eba73d6fcb361b7bdb4fd494e9
 # sha256 is the preferred checksum -- you can get it for a file with:
 #  `openssl sha256 <file name>`.
 # You may need the openssl package, available on conda-forge:
 #  `conda install openssl -c conda-forge``

 build:
 script: python -m pip install . -vv
 number: 1
 # Uncomment the following line if the package is pure Python and the recipe is exactly the same for all platforms.
 # It is okay if the dependencies are not built for all platforms/versions, although selectors are still not allowed.
 # See https://conda-forge.org/docs/maintainer/knowledge_base.html#noarch-python for more details.
 noarch: python
 # If the installation is complex, or different between Unix and Windows, use separate bld.bat and build.sh files instead of this key.
 # By default, the package will be built for the Python versions supported by conda-forge and for all major OSs.
 # Add the line "skip: True  # [py<35]" (for example) to limit to Python 3.5 and newer, or "skip: True  # [not win]" to limit to Windows.
 # More info about selectors can be found in the conda-build docs:
 # https://docs.conda.io/projects/conda-build/en/latest/resources/define-metadata.html#preprocessing-selectors


 requirements:
 host:
     - python <3.11
     - pip
     - setuptools
     - setuptools-scm
 run:
     - python<3.11
     - biotite
     - scikit-learn
     - numpy<1.24
     - scipy
     - matplotlib-base
     - numba
     - statsmodels

 test:
 # Some packages might need a `test/commands` key to check CLI.
 # List all the packages/modules that `run_test.py` imports.
 imports:
     - pyCapsid
 # For python packages, it is useful to run pip check. However, sometimes the
 # metadata used by pip is out of date. Thus this section is optional if it is
 # failing.
 requires:
     - pip

 about:
 home: https://github.com/luquelab/pycapsid
 summary: A set of computational tools written in python for the analysis of viral capsids
 # Remember to specify the license variants for BSD, Apache, GPL, and LGPL.
 # Use the SPDX identifier, e.g: GPL-2.0-only instead of GNU General Public License version 2.0
 # See https://spdx.org/licenses/
 license: MIT
 # The license_family, i.e. "BSD" if license is "BSD-3-Clause".
 # Optional
 license_family: MIT
 # It is required to include a license file in the package,
 # (even if the license doesn't require it) using the license_file entry.
 # Please also note that some projects have multiple license files which all need to be added using a valid yaml list.
 # See https://docs.conda.io/projects/conda-build/en/latest/resources/define-metadata.html#license-file
 license_file: LICENSE.txt
 # The doc_url and dev_url are optional.
 #doc_url: https://simplejson.readthedocs.io/
 #dev_url: https://github.com/simplejson/simplejson

 extra:
 recipe-maintainers:
     - colintravisbrown
 #    # GitHub IDs for maintainers of the recipe.
 #    # Always check with the people listed below if they are OK becoming maintainers of the recipe. (There will be spam!)
 #    - LisaSimpson
 #    - LandoCalrissian

Write build script files build.sh and bls.bat if noarch: python is not included.
- build.sh—Shell script for macOS and Linux.
- bld.bat—Batch file for Windows.
- The 2 files build.sh and bld.bat must be in the same directory as your meta.yaml file.
bld.bat
- Type exactly as shown below in bld.bat
```
  "%PYTHON%" setup.py install
  if errorlevel 1 exit 1  
```
build.sh
- Type exactly as shown below in build.sh
```
  $PYTHON setup.py install     # Python command to install the script.
```
Building and Installing
- Run conda-build:
```
  conda-build click
```
- If the package has dependencies, link the channel containing them when doing conda build.
```
  conda build -c conda-forge --output-folder .
```
- When conda-build is finished, it displays the package filename and location.
- Install your newly built program on your local computer by using the use-local flag:
```
  conda install --use-local click
```
Uploading new packages to Anaconda.org
- Open an account on Anaconda.org.
- Run the command conda install anaconda-client, enter your username and password.
- Log into your Anaconda.org account with the command:
```
  anaconda login
```
- Upload your package to Anaconda.org
```
  anaconda upload ~/miniconda/conda-bld/linux-64/click-7.0-py37_0.tar.bz2
```

Installing the package after uploading it

First, create a new virtual environment using conda and then activate it.

  conda create -n envName python=3.10 -y
  conda activate envName

  conda install -c account_name -c conda-forge package-name