diff --git a/CHANGELOG.md b/CHANGELOG.md index 24fc7bd..8068740 100644 --- a/CHANGELOG.md +++ b/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] diff --git a/README.md b/README.md index 66cc18b..0f915a3 100644 --- a/README.md +++ b/README.md @@ -97,10 +97,13 @@ 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. @@ -108,3 +111,21 @@ $ pytest # test 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 \ No newline at end of file diff --git a/environment.yml b/environment.yml index 1c72d47..ec69fa3 100644 --- a/environment.yml +++ b/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 \ No newline at end of file