Merge pull request #67 from SchriderLab/ts-dev

Major update: Flexible configs and selection coefficients

Author: Logan Whitehouse

blinx.yaml

@@ -6,99 +6,97 @@ channels:
 dependencies:
   - _libgcc_mutex=0.1=conda_forge
   - _openmp_mutex=4.5=2_gnu
-  - abseil-cpp=20210324.2=h9c3ff4c_0
-  - absl-py=0.15.0=pyhd8ed1ab_0
-  - aiohttp=3.8.1=py39hb9d737c_1
+  - abseil-cpp=20211102.0=h27087fc_1
+  - absl-py=1.2.0=pyhd8ed1ab_0
+  - aiohttp=3.8.1=py310h5764c6d_1
   - aiosignal=1.2.0=pyhd8ed1ab_0
-  - alsa-lib=1.2.3.2=h166bdaf_0
+  - alsa-lib=1.2.6.1=h7f98852_0
   - asciitree=0.3.3=py_2
   - astunparse=1.6.3=pyhd8ed1ab_0
   - async-timeout=4.0.2=pyhd8ed1ab_0
   - attr=2.5.1=h166bdaf_0
-  - attrs=21.4.0=pyhd8ed1ab_0
-  - bcftools=1.15.1=h0ea216a_0
+  - attrs=22.1.0=pyh71513ae_1
   - blinker=1.4=py_1
-  - bokeh=2.3.3=py39hf3d152e_0
+  - bokeh=2.4.3=py310hff52083_0
   - brotli=1.0.9=h166bdaf_7
   - brotli-bin=1.0.9=h166bdaf_7
-  - brotlipy=0.7.0=py39hb9d737c_1004
+  - brotlipy=0.7.0=py310h5764c6d_1004
   - bzip2=1.0.8=h7f98852_4
   - c-ares=1.18.1=h7f98852_0
-  - ca-certificates=2022.5.18.1=ha878542_0
+  - ca-certificates=2022.6.15=ha878542_0
   - cached-property=1.5.2=hd8ed1ab_1
   - cached_property=1.5.2=pyha770c72_1
-  - cachetools=4.2.4=pyhd8ed1ab_0
-  - certifi=2022.5.18.1=py39hf3d152e_0
-  - cffi=1.15.0=py39h4bc2ebd_0
-  - charset-normalizer=2.0.12=pyhd8ed1ab_0
-  - click=8.1.3=py39hf3d152e_0
-  - cloudpickle=2.0.0=pyhd8ed1ab_0
-  - cryptography=36.0.2=py39hd97740a_1
-  - cudatoolkit=11.0.3=h15472ef_10
-  - cudnn=8.2.1.32=h86fa8c9_0
+  - cachetools=5.0.0=pyhd8ed1ab_0
+  - certifi=2022.6.15=py310hff52083_0
+  - cffi=1.15.1=py310h255011f_0
+  - charset-normalizer=2.1.0=pyhd8ed1ab_0
+  - click=8.1.3=py310hff52083_0
+  - cloudpickle=2.1.0=pyhd8ed1ab_0
+  - colorama=0.4.5=pyhd8ed1ab_0
+  - cryptography=37.0.4=py310h597c629_0
   - cycler=0.11.0=pyhd8ed1ab_0
-  - cytoolz=0.11.2=py39hb9d737c_2
-  - dask=2022.2.1=pyhd8ed1ab_0
-  - dask-core=2022.2.1=pyhd8ed1ab_0
+  - cytoolz=0.12.0=py310h5764c6d_0
+  - dask=2022.8.0=pyhd8ed1ab_0
+  - dask-core=2022.8.0=pyhd8ed1ab_0
   - dbus=1.13.6=h5008d03_3
-  - distributed=2022.2.1=pyhd3eb1b0_0
+  - distributed=2022.8.0=pyhd8ed1ab_0
+  - entrypoints=0.4=pyhd8ed1ab_0
   - expat=2.4.8=h27087fc_0
   - fasteners=0.17.3=pyhd8ed1ab_0
-  - fftw=3.3.10=nompi_h77c792f_102
+  - fftw=3.3.10=nompi_ha7695d1_103
   - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
   - font-ttf-inconsolata=3.000=h77eed37_0
   - font-ttf-source-code-pro=2.038=h77eed37_0
   - font-ttf-ubuntu=0.83=hab24e00_0
   - fontconfig=2.14.0=h8e229c2_0
   - fonts-conda-ecosystem=1=0
   - fonts-conda-forge=1=0
-  - fonttools=4.33.3=py39hb9d737c_0
+  - fonttools=4.34.4=py310h5764c6d_0
   - freetype=2.10.4=h0708190_1
-  - frozenlist=1.3.0=py39hb9d737c_1
-  - fsspec=2022.3.0=pyhd8ed1ab_0
+  - frozenlist=1.3.1=py310h5764c6d_0
+  - fsspec=2022.7.1=pyhd8ed1ab_0
   - gast=0.4.0=pyh9f0ad1d_0
   - gettext=0.19.8.1=h73d1719_1008
   - giflib=5.2.1=h36c2ea0_2
-  - google-auth=1.35.0=pyh6c4a22f_0
+  - glib=2.72.1=h6239696_0
+  - glib-tools=2.72.1=h6239696_0
+  - google-auth=2.10.0=pyh6c4a22f_0
   - google-auth-oauthlib=0.4.6=pyhd8ed1ab_0
   - google-pasta=0.2.0=pyh8c360ce_0
-  - grpc-cpp=1.41.1=h75e9d12_2
-  - grpcio=1.41.1=py39hff7568b_1
-  - gsl=2.7=he838d99_0
-  - gst-plugins-base=1.18.5=hf529b03_3
-  - gstreamer=1.20.2=hd4edc92_1
-  - h5py=3.1.0=nompi_py39h25020de_100
-  - hdf5=1.10.6=nompi_h6a2412b_1114
+  - grpc-cpp=1.46.3=hbd84cd8_2
+  - grpcio=1.46.3=py310ha0b7d45_2
+  - gst-plugins-base=1.20.3=hf6a322e_0
+  - gstreamer=1.20.3=hd4edc92_0
+  - h5py=3.7.0=nompi_py310h06dffec_100
+  - hdf5=1.12.1=nompi_h2386368_104
   - heapdict=1.0.1=py_0
-  - htslib=1.15.1=h9753748_0
-  - icu=69.1=h9c3ff4c_0
+  - icu=70.1=h27087fc_0
   - idna=3.3=pyhd8ed1ab_0
-  - importlib-metadata=4.11.3=py39hf3d152e_1
-  - jack=1.9.18=hfd4fe87_1001
-  - jbig=2.1=h7f98852_2003
-  - jinja2=3.1.2=pyhd8ed1ab_0
+  - importlib-metadata=4.11.4=py310hff52083_0
+  - jack=1.9.18=h8c3723f_1002
+  - jinja2=3.1.2=pyhd8ed1ab_1
   - joblib=1.1.0=pyhd8ed1ab_0
-  - jpeg=9e=h166bdaf_1
-  - json-c=0.15=h98cffda_0
-  - keras=2.6.0=pyhd8ed1ab_1
+  - jpeg=9e=h166bdaf_2
+  - keras=2.9.0=pyhd8ed1ab_0
   - keras-preprocessing=1.1.2=pyhd8ed1ab_0
   - keyutils=1.6.1=h166bdaf_0
-  - kiwisolver=1.4.2=py39hf939315_1
+  - kiwisolver=1.4.4=py310hbf28c38_0
   - krb5=1.19.3=h3790be6_0
   - lcms2=2.12=hddcbb42_0
   - ld_impl_linux-64=2.36.1=hea4e1c9_2
-  - lerc=3.0=h9c3ff4c_0
-  - libblas=3.9.0=14_linux64_openblas
+  - lerc=4.0.0=h27087fc_0
+  - libblas=3.9.0=15_linux64_openblas
   - libbrotlicommon=1.0.9=h166bdaf_7
   - libbrotlidec=1.0.9=h166bdaf_7
   - libbrotlienc=1.0.9=h166bdaf_7
-  - libcap=2.51=h166bdaf_1
-  - libcblas=3.9.0=14_linux64_openblas
-  - libclang=13.0.1=default_hc23dcda_0
+  - libcap=2.64=ha37c62d_0
+  - libcblas=3.9.0=15_linux64_openblas
+  - libclang=14.0.6=default_h2e3cab8_0
+  - libclang13=14.0.6=default_h3a83d3e_0
   - libcups=2.3.3=hf5a7f15_1
   - libcurl=7.83.1=h7bff187_0
   - libdb=6.2.32=h9c3ff4c_0
-  - libdeflate=1.10=h7f98852_0
+  - libdeflate=1.13=h166bdaf_0
   - libedit=3.1.20191231=he28a2e2_2
   - libev=4.33=h516909a_1
   - libevent=2.1.10=h9b69904_4
@@ -107,145 +105,139 @@ dependencies:
   - libgcc-ng=12.1.0=h8d9b700_16
   - libgfortran-ng=12.1.0=h69a702a_16
   - libgfortran5=12.1.0=hdcd56e2_16
-  - libglib=2.70.2=h174f98d_4
+  - libglib=2.72.1=h2d90d5f_0
   - libgomp=12.1.0=h8d9b700_16
   - libiconv=1.16=h516909a_0
-  - liblapack=3.9.0=14_linux64_openblas
-  - libllvm13=13.0.1=hf817b99_2
+  - liblapack=3.9.0=15_linux64_openblas
+  - libllvm14=14.0.6=he0ac6c6_0
   - libnghttp2=1.47.0=h727a467_0
   - libnsl=2.0.0=h7f98852_0
   - libogg=1.3.4=h7f98852_1
-  - libopenblas=0.3.20=pthreads_h78a6416_0
+  - libopenblas=0.3.20=pthreads_h78a6416_1
   - libopus=1.3.1=h7f98852_1
-  - libpng=1.6.37=h21135ba_2
-  - libpq=14.3=hd77ab85_0
-  - libprotobuf=3.18.1=h780b84a_0
+  - libpng=1.6.37=h753d276_3
+  - libpq=14.4=hd77ab85_0
+  - libprotobuf=3.20.1=h6239696_0
   - libsndfile=1.0.31=h9c3ff4c_1
   - libssh2=1.10.0=ha56f1ee_2
   - libstdcxx-ng=12.1.0=ha89aaad_16
-  - libtiff=4.3.0=h542a066_3
+  - libtiff=4.4.0=h0e0dad5_3
   - libtool=2.4.6=h9c3ff4c_1008
+  - libudev1=249=h166bdaf_4
   - libuuid=2.32.1=h7f98852_1000
   - libvorbis=1.3.7=h9c3ff4c_0
-  - libwebp=1.2.2=h3452ae3_0
-  - libwebp-base=1.2.2=h7f98852_1
+  - libwebp=1.2.3=h522a892_1
+  - libwebp-base=1.2.3=h166bdaf_2
   - libxcb=1.13=h7f98852_1004
   - libxkbcommon=1.0.3=he3ba5ed_0
-  - libxml2=2.9.12=h885dcf4_1
-  - libzlib=1.2.11=h166bdaf_1014
+  - libxml2=2.9.14=h22db469_3
+  - libzlib=1.2.12=h166bdaf_2
   - locket=1.0.0=pyhd8ed1ab_0
+  - lz4=4.0.0=py310h5d5e884_2
   - lz4-c=1.9.3=h9c3ff4c_1
-  - markdown=3.3.7=pyhd8ed1ab_0
-  - markupsafe=2.1.1=py39hb9d737c_1
-  - matplotlib=3.5.2=py39hf3d152e_0
-  - matplotlib-base=3.5.2=py39h700656a_0
-  - msgpack-python=1.0.3=py39hf939315_1
-  - multidict=6.0.2=py39hb9d737c_1
+  - markdown=3.4.1=pyhd8ed1ab_0
+  - markupsafe=2.1.1=py310h5764c6d_1
+  - matplotlib=3.5.2=py310hff52083_1
+  - matplotlib-base=3.5.2=py310h5701ce4_1
+  - msgpack-python=1.0.4=py310hbf28c38_0
+  - multidict=6.0.2=py310h5764c6d_1
   - munkres=1.1.4=pyh9f0ad1d_0
-  - mysql-common=8.0.29=haf5c9bc_0
-  - mysql-libs=8.0.29=h28c427c_0
-  - nccl=2.12.12.1=h17a0586_0
+  - mysql-common=8.0.30=haf5c9bc_0
+  - mysql-libs=8.0.30=h28c427c_0
   - ncurses=6.3=h27087fc_1
-  - networkx=2.8=pyhd8ed1ab_0
+  - networkx=2.8.5=pyhd8ed1ab_0
   - nomkl=1.0=h5ca1d4c_0
   - nspr=4.32=h9c3ff4c_1
-  - nss=3.77=h2350873_0
-  - numcodecs=0.9.1=py39he80948d_2
-  - numexpr=2.8.0=py39h194a79d_102
-  - numpy=1.19.5=py39hd249d9e_3
+  - nss=3.78=h2350873_0
+  - numcodecs=0.10.2=py310hd8f1fbe_0
+  - numexpr=2.8.3=py310hf05e7a9_100
+  - numpy=1.23.1=py310h53a5b5f_0
   - oauthlib=3.2.0=pyhd8ed1ab_0
   - openjpeg=2.4.0=hb52868f_1
-  - openssl=1.1.1o=h166bdaf_0
+  - openssl=1.1.1q=h166bdaf_0
   - opt_einsum=3.3.0=pyhd8ed1ab_1
   - packaging=21.3=pyhd8ed1ab_0
-  - pandas=1.4.2=py39h1832856_1
+  - pandas=1.4.3=py310h769672d_0
   - partd=1.2.0=pyhd8ed1ab_0
   - patsy=0.5.2=pyhd8ed1ab_0
   - pcre=8.45=h9c3ff4c_0
-  - perl=5.32.1=2_h7f98852_perl5
-  - pillow=9.1.0=py39hae2aec6_2
-  - pip=22.1.1=pyhd8ed1ab_0
-  - pomegranate=0.13.3=py39h081fc7a_1
-  - protobuf=3.18.1=py39he80948d_0
-  - psutil=5.9.0=py39hb9d737c_1
+  - pillow=9.2.0=py310he619898_0
+  - pip=22.2.2=pyhd8ed1ab_0
+  - ply=3.11=py_1
+  - pomegranate=0.13.3=py310h91b1402_3
+  - portaudio=19.6.0=h57a0ea0_5
+  - protobuf=3.20.1=py310hd8f1fbe_0
+  - psutil=5.9.1=py310h5764c6d_0
   - pthread-stubs=0.4=h36c2ea0_1001
-  - pulseaudio=14.0=hb166930_4
+  - pulseaudio=14.0=h7f54b18_8
   - pyasn1=0.4.8=py_0
   - pyasn1-modules=0.2.7=py_0
   - pycparser=2.21=pyhd8ed1ab_0
   - pyjwt=2.4.0=pyhd8ed1ab_0
   - pyopenssl=22.0.0=pyhd8ed1ab_0
   - pyparsing=3.0.9=pyhd8ed1ab_0
-  - pyqt=5.15.4=py39h5a03fae_0
-  - pyqt5-sip=12.9.0=py39h5a03fae_0
-  - pysocks=1.7.1=py39hf3d152e_5
-  - python=3.9.12=h9a8a25e_1_cpython
+  - pyqt=5.15.7=py310h29803b5_0
+  - pyqt5-sip=12.11.0=py310hd8f1fbe_0
+  - pysocks=1.7.1=py310hff52083_5
+  - python=3.10.5=h582c2e5_0_cpython
   - python-dateutil=2.8.2=pyhd8ed1ab_0
   - python-flatbuffers=1.12=pyhd8ed1ab_1
-  - python_abi=3.9=2_cp39
+  - python_abi=3.10=2_cp310
   - pytz=2022.1=pyhd8ed1ab_0
   - pyu2f=0.1.5=pyhd8ed1ab_0
-  - pyyaml=6.0=py39hb9d737c_4
-  - qt-main=5.15.2=hdf1cb14_3
-  - re2=2021.11.01=h9c3ff4c_0
-  - readline=8.1=h46c0cb4_0
-  - requests=2.27.1=pyhd8ed1ab_0
+  - pyyaml=6.0=py310h5764c6d_4
+  - qt-main=5.15.4=ha5833f6_2
+  - re2=2022.06.01=h27087fc_0
+  - readline=8.1.2=h0f457ee_0
+  - requests=2.28.1=pyhd8ed1ab_0
   - requests-oauthlib=1.3.1=pyhd8ed1ab_0
-  - rsa=4.8=pyhd8ed1ab_0
-  - samtools=1.15.1=h1170115_0
-  - scikit-allel=1.3.5=py39hde0f152_1
-  - scikit-learn=1.1.0=py39h4037b75_0
-  - scipy=1.8.0=py39hee8e79c_1
+  - rsa=4.9=pyhd8ed1ab_0
+  - scikit-allel=1.3.5=py310hb5077e9_1
+  - scikit-learn=1.1.2=py310h0c3af53_0
+  - scipy=1.9.0=py310hdfbd76f_0
   - seaborn=0.11.2=hd8ed1ab_0
   - seaborn-base=0.11.2=pyhd8ed1ab_0
-  - setuptools=62.2.0=py39hf3d152e_0
-  - sip=6.5.1=py39he80948d_2
-  - six=1.15.0=pyh9f0ad1d_0
-  - slim=3.7.1=h9c3ff4c_1
-  - snappy=1.1.9=hbd366e4_0
+  - setuptools=63.4.2=py310hff52083_0
+  - sip=6.6.2=py310hd8f1fbe_0
+  - six=1.16.0=pyh6c4a22f_0
+  - snappy=1.1.9=hbd366e4_1
   - sortedcontainers=2.4.0=pyhd8ed1ab_0
-  - sqlite=3.38.5=h4ff8645_0
-  - statsmodels=0.13.2=py39hce5d2b2_0
+  - sqlite=3.39.2=h4ff8645_0
+  - statsmodels=0.13.2=py310hde88566_0
   - tblib=1.7.0=pyhd8ed1ab_0
-  - tensorboard=2.6.0=pyhd8ed1ab_1
-  - tensorboard-data-server=0.6.0=py39hd97740a_2
+  - tensorboard=2.9.0=pyhd8ed1ab_0
+  - tensorboard-data-server=0.6.0=py310h597c629_2
   - tensorboard-plugin-wit=1.8.1=pyhd8ed1ab_0
-  - tensorflow=2.6.2=cuda110py39h016931e_1
-  - tensorflow-base=2.6.2=cuda110py39h405f49e_1
-  - tensorflow-estimator=2.6.2=cuda110py39h016931e_1
-  - tensorflow-gpu=2.6.2=cuda110py39h5b0ac8e_1
-  - termcolor=1.1.0=py_2
+  - tensorflow=2.9.1=cpu_py310hd1aba9c_0
+  - tensorflow-base=2.9.1=cpu_py310h8df3ab6_0
+  - tensorflow-estimator=2.9.1=cpu_py310had6d012_0
+  - termcolor=1.1.0=pyhd8ed1ab_3
   - threadpoolctl=3.1.0=pyh8a188c0_0
   - tk=8.6.12=h27826a3_0
   - toml=0.10.2=pyhd8ed1ab_0
-  - toolz=0.11.2=pyhd8ed1ab_0
-  - tornado=6.1=py39hb9d737c_3
-  - tqdm=4.64.0=py39h06a4308_0
+  - toolz=0.12.0=pyhd8ed1ab_0
+  - tornado=6.1=py310h5764c6d_3
+  - tqdm=4.64.0=pyhd8ed1ab_0
+  - typing-extensions=4.3.0=hd8ed1ab_0
+  - typing_extensions=4.3.0=pyha770c72_0
   - tzdata=2022a=h191b570_0
-  - unicodedata2=14.0.0=py39hb9d737c_1
-  - urllib3=1.26.9=pyhd8ed1ab_0
-  - werkzeug=2.1.2=pyhd8ed1ab_1
+  - unicodedata2=14.0.0=py310h5764c6d_1
+  - urllib3=1.26.11=pyhd8ed1ab_0
+  - werkzeug=2.2.1=pyhd8ed1ab_0
   - wheel=0.37.1=pyhd8ed1ab_0
-  - wrapt=1.12.1=py39h3811e60_3
+  - wrapt=1.14.1=py310h5764c6d_0
+  - xcb-util=0.4.0=h516909a_0
+  - xcb-util-image=0.4.0=h166bdaf_0
+  - xcb-util-keysyms=0.4.0=h516909a_0
+  - xcb-util-renderutil=0.3.9=h166bdaf_0
+  - xcb-util-wm=0.4.1=h516909a_0
   - xorg-libxau=1.0.9=h7f98852_0
   - xorg-libxdmcp=1.1.3=h7f98852_0
   - xz=5.2.5=h516909a_1
   - yaml=0.2.5=h7f98852_2
-  - yarl=1.7.2=py39hb9d737c_2
-  - zarr=2.11.3=pyhd8ed1ab_0
+  - yarl=1.7.2=py310h5764c6d_2
+  - zarr=2.12.0=pyhd8ed1ab_0
   - zict=2.2.0=pyhd8ed1ab_0
-  - zipp=3.8.0=pyhd8ed1ab_0
-  - zlib=1.2.11=h166bdaf_1014
-  - zstd=1.5.2=ha95c52a_0
-  - pip:
-    - black==22.3.0
-    - iniconfig==1.1.1
-    - mypy-extensions==0.4.3
-    - pathspec==0.9.0
-    - platformdirs==2.5.2
-    - pluggy==1.0.0
-    - py==1.11.0
-    - pytest==7.1.2
-    - tomli==2.0.1
-    - typing-extensions==4.2.0
-prefix: /home/lswhiteh/miniconda3/envs/blinx
+  - zipp=3.8.1=pyhd8ed1ab_0
+  - zlib=1.2.12=h166bdaf_2
+  - zstd=1.5.2=h8a70e8d_3

examples/example_config.yaml

@@ -1,8 +1,8 @@
 #General
-work dir: example_config
+work dir: example_run
 slimfile: example_model.slim 
 
-scenarios: ["neutral", "hard_sweep", "soft_sweep"]
+scenarios: ["neut", "hard", "soft"]
 mut types: [2]
 sample sizes: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10]
 ploidy: 2

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = Timesweeper
-version = 1.0.0
+version = 1.1.0
 author = Logan Whitehouse
 author_email = lswhiteh@unc.edu
 description = A tool for detecting positive selective sweeps using time-series genomcis data.