From 4a05fb249b8067f6951f07bc62494f0f2cb88611 Mon Sep 17 00:00:00 2001
From: Vini Salazar <viniws@gmail.com>
Date: Fri, 8 Jan 2021 13:17:10 -0300
Subject: [PATCH] Update env file to Py 3.9

---
 CHANGELOG.md    |   1 +
 environment.yml | 232 ++++++++++++++++++++++--------------------------
 2 files changed, 108 insertions(+), 125 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 55e4c63..2e4f79b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,7 @@
 * Add sequence dunder methods for Project class [x]
 * Improve run methods [x]
 * Allow specifying sequence format to PresetProgram outputs [x]
+* Update env file to Py 3.9 [x]
 
 ### v0.1.21
 * Add _config argument to `bp.load_project()` (this is a temporary fix) [x]
diff --git a/environment.yml b/environment.yml
index 201861f..a6bb1ca 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,146 +1,128 @@
-name: bioprov
+name: bioprov-dev
 channels:
-  - salilab
   - conda-forge
   - bioconda
   - defaults
 dependencies:
-  - _libgcc_mutex=0.1
-  - _openmp_mutex=4.5
-  - argon2-cffi=20.1.0
-  - async_generator=1.10
-  - attrs=20.2.0
-  - backports=1.0
-  - backports.functools_lru_cache=1.6.1
-  - bleach=3.2.1
-  - brotlipy=0.7.0
-  - ca-certificates=2020.6.20
-  - certifi=2020.6.20
-  - cffi=1.14.3
-  - chardet=3.0.4
-  - cryptography=3.1.1
-  - decorator=4.4.2
-  - defusedxml=0.6.0
-  - entrypoints=0.3
-  - idna=2.10
-  - importlib-metadata=2.0.0
-  - importlib_metadata=2.0.0
-  - ipykernel=5.3.4
-  - ipython=5.8.0
-  - ipython_genutils=0.2.0
-  - jinja2=2.11.2
-  - json5=0.9.5
-  - jsonschema=3.2.0
-  - jupyter_client=6.1.7
-  - jupyter_core=4.6.3
-  - jupyterlab=2.2.8
-  - jupyterlab_pygments=0.1.2
-  - jupyterlab_server=1.2.0
-  - ld_impl_linux-64=2.35
-  - libcxx=11.0.0
-  - libcxxabi=11.0.0
-  - libffi=3.2.1
-  - libgcc-ng=9.3.0
-  - libgomp=9.3.0
-  - libsodium=1.0.18
-  - libstdcxx-ng=9.3.0
-  - markupsafe=1.1.1
-  - mistune=0.8.4
-  - nb_conda_kernels=2.3.0
-  - nbclient=0.5.1
-  - nbconvert=6.0.7
-  - nbformat=5.0.8
-  - ncurses=6.2
-  - nest-asyncio=1.4.1
-  - notebook=6.1.4
-  - openssl=1.1.1h
-  - packaging=20.4
-  - pandoc=2.11.0.2
-  - pandocfilters=1.4.2
-  - pexpect=4.8.0
-  - pickleshare=0.7.5
-  - pip=20.2.3
-  - prodigal=2.6.3
-  - prometheus_client=0.8.0
-  - prompt_toolkit=1.0.15
-  - ptyprocess=0.6.0
-  - pycparser=2.20
-  - pygments=2.7.1
-  - pyopenssl=19.1.0
-  - pyparsing=2.4.7
-  - pyrsistent=0.17.3
-  - pysocks=1.7.1
-  - python=3.7.8
-  - python-dateutil=2.8.1
-  - python_abi=3.7
-  - pyzmq=19.0.2
-  - readline=8.0
-  - requests=2.24.0
-  - send2trash=1.5.0
-  - setuptools=49.6.0
-  - simplegeneric=0.8.1
-  - six=1.15.0
-  - sqlite=3.33.0
-  - terminado=0.9.1
-  - testpath=0.4.4
-  - tk=8.6.10
-  - tornado=6.0.4
-  - traitlets=5.0.5
-  - urllib3=1.25.10
-  - wcwidth=0.2.5
-  - webencodings=0.5.1
-  - wheel=0.35.1
-  - xz=5.2.5
-  - zeromq=4.3.3
-  - zipp=3.3.1
-  - zlib=1.2.11
+  - attrs=20.3.0=pyhd3deb0d_0
+  - bioprov=0.1.20=pyh3252c3a_0
+  - biopython=1.78=py39h4059872_1
+  - brotlipy=0.7.0=py39h66d5b7b_1001
+  - ca-certificates=2020.12.5=h033912b_0
+  - certifi=2020.12.5=py39h6e9494a_1
+  - cffi=1.14.4=py39h7786acb_1
+  - chardet=4.0.0=py39h6e9494a_1
+  - coolname=1.1.0=py39h6e9494a_2
+  - coverage=5.3.1=py39hcbf5805_1
+  - coveralls=2.2.0=pyhd8ed1ab_0
+  - cryptography=3.3.1=py39h79a2c39_0
+  - dataclasses=0.7=pyhb2cacf7_7
+  - decorator=4.4.2=py_0
+  - docopt=0.6.2=py_1
+  - freetype=2.10.4=h3f75d11_0
+  - graphviz=2.42.3=h98dfb87_0
+  - html5lib=1.1=pyh9f0ad1d_0
+  - icu=68.1=h74dc148_0
+  - idna=2.10=pyh9f0ad1d_0
+  - iniconfig=1.1.1=pyh9f0ad1d_0
+  - ipython_genutils=0.2.0=py_1
+  - isodate=0.6.0=py_1
+  - jpeg=9d=hbcb3906_0
+  - jupyter_client=6.1.7=py_0
+  - jupyter_core=4.7.0=py39h6e9494a_0
+  - keepalive=0.5=py39h6e9494a_5
+  - libblas=3.9.0=7_openblas
+  - libcblas=3.9.0=7_openblas
+  - libcxx=11.0.0=h4c3b8ed_1
+  - libffi=3.3=h046ec9c_2
+  - libgfortran=5.0.0=h6c81a4c_15
+  - libgfortran5=9.3.0=h6c81a4c_15
+  - libiconv=1.16=haf1e3a3_0
+  - liblapack=3.9.0=7_openblas
+  - libopenblas=0.3.12=openmp_h54245bb_1
+  - libpng=1.6.37=h7cec526_2
+  - libsodium=1.0.18=hbcb3906_1
+  - libtiff=4.2.0=h355d032_0
+  - libwebp-base=1.1.0=hbcb3906_3
+  - libxml2=2.9.10=h802ca4f_3
+  - libxslt=1.1.33=h5739fc3_2
+  - llvm-openmp=11.0.0=h73239a0_1
+  - lxml=4.6.2=py39h9e3495c_0
+  - lz4-c=1.9.3=h046ec9c_0
+  - more-itertools=8.6.0=pyhd8ed1ab_0
+  - nb_conda_kernels=2.3.1=py39h6e9494a_0
+  - ncurses=6.2=h2e338ed_4
+  - networkx=2.5=py_0
+  - numpy=1.19.5=py39he588a01_0
+  - openssl=1.1.1i=h35c211d_0
+  - packaging=20.8=pyhd3deb0d_0
+  - pandas=1.2.0=py39h089d6f7_0
+  - pip=20.3.3=pyhd8ed1ab_0
+  - pluggy=0.13.1=py39h2c36a5b_3
+  - prodigal=2.6.3=h01d97ff_2
+  - prov=2.0.0=pyhd3deb0d_0
+  - provstore-api=0.1.3=py39h6e9494a_2
+  - py=1.10.0=pyhd3deb0d_0
+  - pycparser=2.20=pyh9f0ad1d_2
+  - pydot=1.4.1=py39h6e9494a_1003
+  - pyopenssl=20.0.1=pyhd8ed1ab_0
+  - pyparsing=2.4.7=pyh9f0ad1d_0
+  - pysocks=1.7.1=py39h2c36a5b_2
+  - pytest=6.2.1=py39h6e9494a_0
+  - pytest-cov=2.10.1=pyh9f0ad1d_0
+  - python=3.9.1=h1d169a7_2_cpython
+  - python-dateutil=2.8.1=py_0
+  - python_abi=3.9=1_cp39
+  - pytz=2020.5=pyhd8ed1ab_0
+  - pyyaml=5.3.1=py39h66d5b7b_1
+  - pyzmq=20.0.0=py39h07c395c_1
+  - rdflib=5.0.0=py39hde42818_3
+  - readline=8.0=h0678c8f_2
+  - requests=2.25.1=pyhd3deb0d_0
+  - setuptools=49.6.0=py39h6e9494a_3
+  - six=1.15.0=pyh9f0ad1d_0
+  - sparqlwrapper=1.8.5=py39h6e9494a_1005
+  - sqlite=3.34.0=h17101e1_0
+  - tinydb=4.3.0=pyhd3deb0d_0
+  - tk=8.6.10=h0419947_1
+  - toml=0.10.2=pyhd8ed1ab_0
+  - tornado=6.1=py39hcbf5805_1
+  - tqdm=4.55.1=pyhd8ed1ab_0
+  - traitlets=5.0.5=py_0
+  - tzdata=2020f=he74cb21_0
+  - urllib3=1.26.2=pyhd8ed1ab_0
+  - webencodings=0.5.1=py_1
+  - wheel=0.36.2=pyhd3deb0d_0
+  - xz=5.2.5=haf1e3a3_1
+  - yaml=0.2.5=haf1e3a3_0
+  - zeromq=4.3.3=h74dc148_3
+  - zlib=1.2.11=h7795811_1010
+  - zstd=1.4.8=hf387650_1
   - pip:
     - alabaster==0.7.12
     - appdirs==1.4.4
-    - babel==2.8.0
-    - bioprov==0.1.13
-    - biopython==1.78
+    - babel==2.9.0
     - black==20.8b1
     - click==7.1.2
-    - coolname==1.1.0
-    - coverage==5.3
-    - coveralls==2.1.2
-    - dataclasses==0.6
-    - docopt==0.6.2
     - docutils==0.16
     - imagesize==1.2.0
-    - iniconfig==1.1.1
-    - isodate==0.6.0
-    - lxml==4.5.2
-    - markdown-it-py==0.5.5
+    - jinja2==2.11.2
+    - markdown-it-py==0.6.1
+    - markupsafe==1.1.1
+    - mdit-py-plugins==0.2.4
     - mypy-extensions==0.4.3
-    - myst-parser==0.12.10
-    - networkx==2.5
-    - numpy==1.19.2
-    - pandas==1.1.3
-    - pathspec==0.8.0
-    - pluggy==0.13.1
-    - prov==1.5.3
-    - provstore-api==0.1.3
-    - py==1.9.0
-    - pydot==1.4.1
-    - pytest==6.1.1
-    - pytest-cov==2.10.1
-    - pytz==2020.1
-    - pyyaml==5.3.1
-    - rdflib==5.0.0
-    - regex==2020.10.15
+    - myst-parser==0.13.1
+    - pathspec==0.8.1
+    - pygments==2.7.3
+    - regex==2020.11.13
     - snowballstemmer==2.0.0
-    - sphinx==3.2.1
-    - sphinx-rtd-theme==0.5.0
+    - sphinx==3.4.3
     - sphinxcontrib-applehelp==1.0.2
     - sphinxcontrib-devhelp==1.0.2
     - sphinxcontrib-htmlhelp==1.0.3
     - sphinxcontrib-jsmath==1.0.1
     - sphinxcontrib-qthelp==1.0.3
     - sphinxcontrib-serializinghtml==1.1.4
-    - tinydb==4.2.0
-    - toml==0.10.1
-    - tqdm==4.50.2
-    - typed-ast==1.4.1
+    - typed-ast==1.4.2
     - typing-extensions==3.7.4.3
+prefix: /Users/vini/anaconda3/envs/new-bp-env