Update environment.yaml

  - Make environment file more concise, use mostly dependencies from setup.py
  - Add dependencies from environment.yaml to README

CHANGELOG.md

@@ -10,7 +10,7 @@
 * Add logger calls when saving to JSON and uploading to ProvStore [ ]
 
 ### v0.1.24
-* State requirements more clearly [ ]
+* State requirements more clearly [x]
 * Improve error handling when getting `Program` attributes [x]
 * Add `__doc__` variable to modules to build documentation [x]
 * Fix `File.size` property [x]

README.md

@@ -97,14 +97,35 @@ You can import data into BioProv using Pandas objects.
 # Install from pip
 $ pip install bioprov
 
-# Or install from source
-$ git clone https://github.com/vinisalazar/bioprov  # download
-$ cd bioprov; pip install .                         # install
-$ pytest                                            # test
+# Install from conda
+$ conda install -c conda-forge -c bioconda bioprov
+
+# Install from source
+$ git clone https://github.com/vinisalazar/bioprov && cd bioprov;     # download
+$ conda env create -f environment.yaml && conda activate bioprov;     # install dependencies
+$ pip install . && pytest;                                            # install and test
 ```
 
 **Important!** BioProv requires [Prodigal](https://github.com/hyattpd/Prodigal) to be tested. Otherwise tests will fail.
 
 Contributions are welcome!
 
 **BioProv is in active development and no warranties are provided (please see the License).**
+
+### Dependencies
+
+BioProv requires the follow dependencies to run. Also see the [setup](./setup.py) and [environment](./environment.yaml) files.
+
+- biopython
+- coolname
+- coveralls
+- dataclasses
+- pandas
+- prodigal
+- prov
+- provstore-api
+- pydot
+- pytest
+- pytest-cov
+- tqdm
+- tinydb

environment.yml

@@ -4,82 +4,16 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - attrs
-  - bioprov
   - biopython
-  - black
-  - brotlipy
-  - ca-certificates
-  - certifi
-  - cffi
-  - chardet
   - coolname
-  - coverage
   - coveralls
-  - cryptography
   - dataclasses
-  - decorator
-  - docopt
-  - html5lib
-  - icu
-  - idna
-  - iniconfig
-  - isodate
-  - jupyterlab
-  - keepalive
-  - libblas
-  - libcblas
-  - libcxx
-  - libffi
-  - libgfortran
-  - libgfortran5
-  - libiconv
-  - liblapack
-  - libopenblas
-  - libxml2
-  - libxslt
-  - llvm-openmp
-  - lxml
-  - more-itertools
-  - ncurses
-  - networkx
-  - numpy
-  - openssl
-  - packaging
   - pandas
-  - pip
-  - pluggy
   - prodigal
   - prov
   - provstore-api
-  - py
-  - pycparser
   - pydot
-  - pyopenssl
-  - pyparsing
-  - pysocks
   - pytest
   - pytest-cov
-  - python
-  - python-dateutil
-  - python_abi
-  - pytz
-  - pyyaml
-  - rdflib
-  - readline
-  - requests
-  - setuptools
-  - six
-  - sparqlwrapper
-  - sqlite
-  - tinydb
-  - tk
-  - toml
   - tqdm
-  - tzdata
-  - urllib3
-  - webencodings
-  - wheel
-  - xz
-  - yaml
-  - zlib
+  - tinydb