Add conda package

.github/workflows/release.yml

@@ -14,7 +14,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: '3.x'
+        python-version: '3.8'
     - name: Install dependencies
       run:
         pip install --upgrade pip flit

README.md

@@ -2,6 +2,7 @@
 
 [![license-badge](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![pypi-badge](https://img.shields.io/pypi/v/scglue)](https://pypi.org/project/scglue)
+[![conda-badge](https://anaconda.org/scglue/scglue/badges/version.svg)](https://anaconda.org/scglue/scglue)
 [![docs-badge](https://readthedocs.org/projects/scglue/badge/?version=latest)](https://scglue.readthedocs.io/en/latest/?badge=latest)
 [![build-badge](https://github.com/gao-lab/GLUE/actions/workflows/build.yml/badge.svg)](https://github.com/gao-lab/GLUE/actions/workflows/build.yml)
 [![coverage-badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/Jeff1995/e704b2f886ff6a37477311b90fdf7efa/raw/coverage.json)](https://github.com/gao-lab/GLUE/actions/workflows/build.yml)
@@ -32,32 +33,34 @@ For more details, please check out our [preprint](https://www.biorxiv.org/conten
 
 ## Package installation
 
-It is recommended to install `scglue` within a
-[conda](https://docs.conda.io/en/latest/miniconda.html) environment.
-
-First, initialize an empty conda environment (here named "scglue"):
+The `scglue` package can be installed either via conda:
 
 ```sh
-conda env create -n scglue "python>=3.6" && conda activate scglue
+conda install -c defaults -c pytorch -c bioconda -c conda-forge -c scglue scglue
 ```
 
-Then, install scglue via:
+Or via pip:
 
 ```sh
 pip install scglue
 ```
 
+> Installing within a
+> [conda environment](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html)
+> is recommended.
+
 ## Package usage
 
 Please checkout the documentations and tutorials at
 [scglue.readthedocs.io](https://scglue.readthedocs.io).
 
 ## Package development
 
-Install scglue in editable form via flit:
+Install scglue in editable form via flit (first install flit via conda or pip
+if not installed already):
 
 ```sh
-pip install flit && flit install -s
+flit install -s
 ```
 
 Run unit tests:

conda-build/README.md

@@ -0,0 +1,8 @@
+# Building the conda package
+
+After updating the recipe, run:
+
+```sh
+conda build -c defaults -c pytorch -c bioconda -c conda-forge scglue
+anaconda upload -u scglue path_to_the_built_package.tar.bz2
+```

conda-build/scglue/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021, Gao Lab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

conda-build/scglue/meta.yaml

@@ -0,0 +1,81 @@
+{% set name = "scglue" %}
+{% set version = "0.1.1" %}  # Update
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
+  sha256: 9e69628800e842c1afd74cc71a0067412404da1cb4f4de063915d2375b81223a  # Update
+
+build:
+  noarch: python
+  number: 0
+  script: "{{ PYTHON }} -m pip install . -vv"
+
+requirements:
+  host:  # Might need update
+    - anndata >=0.7
+    - dill >=0.2.3
+    - flit >=3.2,<4
+    - ignite >=0.4.1
+    - matplotlib >=3.1.2
+    - networkx >=2
+    - numpy >=1.19
+    - pandas >=1.1
+    - parse >=1.3.2
+    - pip
+    - pybedtools >=0.8.1
+    - pynvml >=8.0.1
+    - python >=3.6
+    - pytorch >=1.7
+    - scanpy >=1.5
+    - scikit-learn >=0.21.2
+    - scipy >=1.3
+    - seaborn >=0.9
+    - statsmodels >=0.10
+    - tensorboardx >=1.4
+    - tqdm >=4.27
+  run:  # Might need update
+    - anndata >=0.7
+    - dill >=0.2.3
+    - ignite >=0.4.1
+    - matplotlib >=3.1.2
+    - networkx >=2
+    - numpy >=1.19
+    - pandas >=1.1
+    - parse >=1.3.2
+    - pybedtools >=0.8.1
+    - pynvml >=8.0.1
+    - python >=3.6
+    - pytorch >=1.7
+    - scanpy >=1.5
+    - scikit-learn >=0.21.2
+    - scipy >=1.3
+    - seaborn >=0.9
+    - statsmodels >=0.10
+    - tensorboardx >=1.4
+    - tqdm >=4.27
+
+test:
+  imports:
+    - scglue
+    - scglue.models
+
+about:
+  home: https://github.com/gao-lab/GLUE
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: "Graph-linked unified embedding for unpaired single-cell multi-omics data integration"
+  description: |
+    GLUE is a flexible framework that utilizes prior knowledge about feature
+    relations to bridge the gap between different feature spaces during unpaired
+    multi-modal data integration.
+  doc_url: https://scglue.readthedocs.io
+  dev_url: https://github.com/gao-lab/GLUE
+
+extra:
+  recipe-maintainers:
+    - Jeff1995

docs/install.rst

@@ -5,34 +5,23 @@ Installation guide
 Main package
 ************
 
-It is recommended to install ``scglue`` in a `conda <https://docs.conda.io/en/latest/miniconda.html>`_ environment, to avoid potential dependency conflicts.
-
-First create a new conda environment (here named "scglue", but you may name it whatever you like), and activate it:
+The ``scglue`` package can be installed either via conda:
 
 .. code-block:: bash
     :linenos:
 
-    conda create -n scglue "python>=3.6"
-    conda activate scglue
+    conda install -c defaults -c pytorch -c bioconda -c conda-forge -c scglue scglue
 
-Then install ``scglue`` via:
+Or via pip:
 
 .. code-block:: bash
     :linenos:
 
     pip install scglue
 
-*********************
-Optional dependencies
-*********************
-
-In order to use some of the genomics-related functions, it is necessary to have `bedtools <https://bedtools.readthedocs.io/en/latest/index.html>`_ installed (at least v2.29.2). You may also install it from conda:
-
-.. code-block:: bash
-    :linenos:
-
-    conda install -c bioconda "bedtools>=2.29.2"
-
-.. note:: A conda package is also being prepared, which would be more convenient. Stay tuned.
+.. note::
+    To avoid potential dependency conflicts, installing within a
+    `conda environment <https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html>`_
+    is recommended.
 
 Now you are all set. Proceed to `tutorials <tutorials.rst>`_ for how to use the ``scglue`` package.

env.yaml

@@ -12,6 +12,7 @@ dependencies:
   - aiohttp=3.7.4
   - alabaster=0.7.12
   - amply=0.1.4
+  - anaconda-client=1.8.0
   - anndata=0.7.6
   - anyio=2.2.0
   - appdirs=1.4.4
@@ -49,6 +50,7 @@ dependencies:
   - blosc=1.21.0
   - bokeh=2.3.3
   - boltons=20.2.1
+  - boolean.py=3.7
   - boto3=1.17.27
   - botocore=1.20.28
   - brotlipy=0.7.0
@@ -66,13 +68,16 @@ dependencies:
   - click=7.1.2
   - clikit=0.6.2
   - cloudpickle=1.6.0
+  - clyent=1.2.2
   - coincbc=2.10.5
   - colorama=0.4.3
   - colorlog=5.0.1
   - commonmark=0.9.1
   - conda=4.10.3
   - conda-build=3.21.4
+  - conda-forge-pinning=2021.09.05.11.13.08
   - conda-package-handling=1.7.3
+  - conda-smithy=3.12
   - configargparse=1.4
   - connection_pool=0.0.3
   - cooler=0.8.11
@@ -91,6 +96,7 @@ dependencies:
   - debugpy=1.4.1
   - decorator=4.4.2
   - defusedxml=0.7.1
+  - deprecated=1.2.12
   - dill=0.3.3
   - distlib=0.3.2
   - distributed=2021.4.1
@@ -130,6 +136,7 @@ dependencies:
   - gffutils=0.10.1
   - ghostscript=9.53.3
   - giflib=5.2.1
+  - git=2.32.0
   - gitdb=4.0.5
   - gitpython=3.1.14
   - glib=2.66.7
@@ -185,6 +192,7 @@ dependencies:
   - ipython=7.21.0
   - ipython_genutils=0.2.0
   - ipywidgets=7.6.3
+  - isodate=0.6.0
   - isort=5.7.0
   - itsdangerous=2.0.1
   - jbig=2.1
@@ -195,6 +203,7 @@ dependencies:
   - jmespath=0.10.0
   - joblib=1.0.1
   - jpeg=9d
+  - jq=1.6
   - json5=0.9.5
   - jsonschema=3.2.0
   - jupyter-packaging=0.7.12
@@ -254,6 +263,7 @@ dependencies:
   - libxcb=1.14
   - libxml2=2.9.10
   - libxslt=1.1.33
+  - license-expression=1.2
   - llvm-openmp=12.0.1
   - llvmlite=0.36.0
   - locket=0.2.1
@@ -281,6 +291,7 @@ dependencies:
   - more-itertools=8.7.0
   - mpi=1.0
   - msgpack-python=1.0.2
+  - msrest=0.6.21
   - multidict=5.1.0
   - multiprocess=0.70.12.2
   - mysql-connector-c=6.1.11
@@ -308,11 +319,12 @@ dependencies:
   - oauth2client=4.1.3
   - oauthlib=3.1.0
   - olefile=0.46
+  - oniguruma=6.9.7.1
   - openblas=0.3.13
   - openjpeg=2.4.0
   - openmpi=4.1.0
   - openpyxl=3.0.7
-  - openssl=1.1.1k
+  - openssl=1.1.1l
   - opt_einsum=3.3.0
   - packaging=20.9
   - pairix=0.3.7
@@ -328,6 +340,7 @@ dependencies:
   - patchelf=0.12
   - patsy=0.5.1
   - pcre=8.44
+  - pcre2=10.35
   - peppy=0.31.1
   - perl=5.26.2
   - perl-app-cpanminus=1.7044
@@ -391,11 +404,13 @@ dependencies:
   - pycairo=1.19.1
   - pycosat=0.6.3
   - pycparser=2.20
+  - pycrypto=2.6.1
   - pydeprecate=0.3.1
   - pydocstyle=5.1.1
   - pydot=1.4.1
   - pyfaidx=0.6.1
   - pygenometracks=3.6
+  - pygithub=1.44
   - pygments=2.8.1
   - pygraphviz=1.7
   - pyjwt=1.7.1
@@ -446,13 +461,16 @@ dependencies:
   - ripgrep=12.1.1
   - rope=0.18.0
   - rsa=4.7.2
+  - ruamel.yaml=0.16.12
+  - ruamel.yaml.clib=0.2.2
   - ruamel_yaml=0.15.100
   - s3transfer=0.3.4
   - samtools=1.12
   - scanpy=1.8.1
   - scikit-learn=0.24.1
   - scikit-misc=0.1.3
   - scipy=1.6.1
+  - scrypt=0.8.18
   - scvi-tools=0.9.1
   - seaborn=0.11.1
   - secretstorage=3.3.1
@@ -521,6 +539,7 @@ dependencies:
   - urllib3=1.26.4
   - veracitools=0.1.3
   - virtualenv=20.4.6
+  - vsts-python-api=0.1.22
   - wcwidth=0.2.5
   - webencodings=0.5.1
   - werkzeug=1.0.1
@@ -531,6 +550,7 @@ dependencies:
   - xeus-python=0.12.3
   - xlsxwriter=3.0.1
   - xmlrunner=1.7.7
+  - xmltodict=0.12.0
   - xorg-kbproto=1.0.7
   - xorg-libice=1.0.10
   - xorg-libsm=1.2.3
@@ -547,6 +567,7 @@ dependencies:
   - yaml=0.2.5
   - yapf=0.31.0
   - yarl=1.5.1
+  - yq=2.12.0
   - zeromq=4.3.3
   - zict=2.0.0
   - zipp=3.4.1