From 13d7f41d256418a35f60edc93641379bf5dfe57e Mon Sep 17 00:00:00 2001
From: mortonjt <jamietmorton@gmail.com>
Date: Tue, 8 Mar 2022 14:56:48 -0500
Subject: [PATCH 1/3] updating ci dependencies

---
 ci/conda_requirements.yml | 373 +++++++++++++++++++++++---------------
 1 file changed, 228 insertions(+), 145 deletions(-)

diff --git a/ci/conda_requirements.yml b/ci/conda_requirements.yml
index 63a02d2..33ea240 100644
--- a/ci/conda_requirements.yml
+++ b/ci/conda_requirements.yml
@@ -1,153 +1,236 @@
+name: deepblast2
 channels:
-  - pytorch
+  - biobakery
   - conda-forge
+  - bioconda
   - defaults
 dependencies:
-  - bzip2=1.0.8=h516909a_0
-  - cffi=1.12.3=py37h8022711_0
-  - cycler=0.10.0=py_1
-  - freetype=2.10.0=he983fc9_1
-  - icu=64.2=he1b5a44_1
-  - joblib=0.13.2=py_0
-  - kiwisolver=1.1.0=py37hc9558a2_0
-  - libblas=3.8.0=12_openblas
-  - libcblas=3.8.0=12_openblas
-  - libffi=3.2.1=he1b5a44_1006
-  - liblapack=3.8.0=12_openblas
-  - libopenblas=0.3.7=h6e990d7_1
-  - libpng=1.6.37=hed695b0_0
-  - matplotlib-base=3.1.1=py37he7580a8_1
-  - ncurses=6.1=hf484d3e_1002
-  - ninja=1.9.0=h6bb024c_0
-  - pandas=0.25.1=py37hb3f55d8_0
-  - patsy=0.5.1=py_0
-  - pip=19.2.3=py37_0
-  - pycparser=2.19=py37_1
-  - pyparsing=2.4.2=py_0
-  - python=3.7.3=h33d41f4_1
-  - python-dateutil=2.8.0=py_0
-  - pytz=2019.2=py_0
-  - readline=8.0=hf8c457e_0
-  - scikit-learn=0.21.3=py37hcdab131_0
-  - seaborn=0.9.0=py_1
-  - setuptools=41.2.0=py37_0
-  - six=1.12.0=py37_1000
-  - sqlite=3.29.0=hcee41ef_1
-  - statsmodels=0.10.1=py37hc1659b7_0
-  - tk=8.6.9=hed695b0_1002
-  - tornado=6.0.3=py37h516909a_0
-  - tqdm=4.35.0=py_0
-  - wheel=0.33.6=py37_0
-  - xz=5.2.4=h14c3975_1001
-  - zlib=1.2.11=h516909a_1005
-  - _libgcc_mutex=0.1=main
-  - backcall=0.1.0=py37_0
-  - biopython=1.76=py37h7b6447c_0
-  - blas=1.0=openblas
-  - ca-certificates=2020.1.1=0
-  - certifi=2020.4.5.1=py37_0
-  - cudatoolkit=10.0.130=0
-  - decorator=4.4.0=py37_1
-  - flake8=3.8.2=py_0
-  - importlib-metadata=1.6.0=py37_0
-  - intel-openmp=2019.4=243
-  - ipython=7.8.0=py37h39e3cac_0
-  - ipython_genutils=0.2.0=py37_0
-  - jedi=0.15.1=py37_0
-  - libgcc-ng=9.1.0=hdf63c60_0
-  - libgfortran-ng=7.3.0=hdf63c60_0
-  - libstdcxx-ng=9.1.0=hdf63c60_0
-  - mccabe=0.6.1=py37_1
-  - mkl=2019.4=243
-  - numpy=1.18.1=py37h94c655d_0
-  - numpy-base=1.18.1=py37h2f8d375_1
-  - openssl=1.1.1g=h7b6447c_0
-  - parso=0.5.1=py_0
-  - pexpect=4.7.0=py37_0
-  - pickleshare=0.7.5=py37_0
-  - prompt_toolkit=2.0.10=py_0
-  - ptyprocess=0.6.0=py37_0
-  - pycodestyle=2.6.0=py_0
-  - pyflakes=2.2.0=py_0
-  - pygments=2.4.2=py_0
-  - scipy=1.4.1=py37habc2bb6_0
-  - traitlets=4.3.3=py37_0
-  - wcwidth=0.1.7=py37_0
-  - zipp=3.1.0=py_0
-  - pytorch=1.4.0=py3.7_cuda10.0.130_cudnn7.6.3_0
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=1_gnu
+  - alsa-lib=1.2.3=h516909a_0
+  - argon2-cffi=21.3.0=pyhd8ed1ab_0
+  - argon2-cffi-bindings=21.2.0=py39h3811e60_1
+  - asttokens=2.0.5=pyhd8ed1ab_0
+  - attrs=21.4.0=pyhd8ed1ab_0
+  - backcall=0.2.0=pyh9f0ad1d_0
+  - backports=1.0=py_2
+  - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
+  - biopython=1.79=py39h3811e60_1
+  - bleach=4.1.0=pyhd8ed1ab_0
+  - brotli=1.0.9=h7f98852_6
+  - brotli-bin=1.0.9=h7f98852_6
+  - bzip2=1.0.8=h7f98852_4
+  - ca-certificates=2021.10.8=ha878542_0
+  - certifi=2021.10.8=py39hf3d152e_1
+  - cffi=1.15.0=py39h4bc2ebd_0
+  - cycler=0.11.0=pyhd8ed1ab_0
+  - dbus=1.13.6=h5008d03_3
+  - debugpy=1.5.1=py39he80948d_0
+  - decorator=5.1.1=pyhd8ed1ab_0
+  - defusedxml=0.7.1=pyhd8ed1ab_0
+  - entrypoints=0.4=pyhd8ed1ab_0
+  - executing=0.8.3=pyhd8ed1ab_0
+  - expat=2.4.6=h27087fc_0
+  - flit-core=3.7.1=pyhd8ed1ab_0
+  - 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=2.13.96=ha180cfb_0
+  - fonts-conda-ecosystem=1=0
+  - fonts-conda-forge=1=0
+  - fonttools=4.29.1=py39h3811e60_0
+  - freetype=2.10.4=h0708190_1
+  - gettext=0.19.8.1=h73d1719_1008
+  - giflib=5.2.1=h36c2ea0_2
+  - gst-plugins-base=1.18.5=hf529b03_3
+  - gstreamer=1.18.5=h9f60fe5_3
+  - hmmer=3.3.2=h87f3376_2
+  - icu=69.1=h9c3ff4c_0
+  - importlib-metadata=4.11.2=py39hf3d152e_0
+  - importlib_resources=5.4.0=pyhd8ed1ab_0
+  - ipykernel=6.9.1=py39hef51801_0
+  - ipython=8.1.1=py39hf3d152e_0
+  - ipython_genutils=0.2.0=py_1
+  - ipywidgets=7.6.5=pyhd8ed1ab_0
+  - jbig=2.1=h7f98852_2003
+  - jedi=0.18.1=py39hf3d152e_0
+  - jinja2=3.0.3=pyhd8ed1ab_0
+  - jpeg=9e=h7f98852_0
+  - jsonschema=4.4.0=pyhd8ed1ab_0
+  - jupyter=1.0.0=py39hf3d152e_7
+  - jupyter_client=7.1.2=pyhd8ed1ab_0
+  - jupyter_console=6.4.3=pyhd8ed1ab_0
+  - jupyter_core=4.9.2=py39hf3d152e_0
+  - jupyterlab_pygments=0.1.2=pyh9f0ad1d_0
+  - jupyterlab_widgets=1.0.2=pyhd8ed1ab_0
+  - keyutils=1.6.1=h166bdaf_0
+  - kiwisolver=1.3.2=py39h1a9c180_1
+  - krb5=1.19.2=h3790be6_4
+  - lcms2=2.12=hddcbb42_0
+  - ld_impl_linux-64=2.36.1=hea4e1c9_2
+  - lerc=3.0=h9c3ff4c_0
+  - libblas=3.9.0=13_linux64_openblas
+  - libbrotlicommon=1.0.9=h7f98852_6
+  - libbrotlidec=1.0.9=h7f98852_6
+  - libbrotlienc=1.0.9=h7f98852_6
+  - libcblas=3.9.0=13_linux64_openblas
+  - libclang=13.0.1=default_hc23dcda_0
+  - libdeflate=1.10=h7f98852_0
+  - libedit=3.1.20191231=he28a2e2_2
+  - libevent=2.1.10=h9b69904_4
+  - libffi=3.4.2=h7f98852_5
+  - libgcc-ng=11.2.0=h1d223b6_13
+  - libgfortran-ng=11.2.0=h69a702a_13
+  - libgfortran5=11.2.0=h5c6108e_13
+  - libglib=2.70.2=h174f98d_4
+  - libgomp=11.2.0=h1d223b6_13
+  - libiconv=1.16=h516909a_0
+  - liblapack=3.9.0=13_linux64_openblas
+  - libllvm11=11.1.0=hf817b99_3
+  - libllvm13=13.0.1=hf817b99_2
+  - libnsl=2.0.0=h7f98852_0
+  - libogg=1.3.4=h7f98852_1
+  - libopenblas=0.3.18=pthreads_h8fe5266_0
+  - libopus=1.3.1=h7f98852_1
+  - libpng=1.6.37=h21135ba_2
+  - libpq=14.2=hd57d9b9_0
+  - libsodium=1.0.18=h36c2ea0_1
+  - libstdcxx-ng=11.2.0=he4da1e4_13
+  - libtiff=4.3.0=h542a066_3
+  - 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
+  - libxcb=1.13=h7f98852_1004
+  - libxkbcommon=1.0.3=he3ba5ed_0
+  - libxml2=2.9.12=h885dcf4_1
+  - libzlib=1.2.11=h36c2ea0_1013
+  - llvmlite=0.38.0=py39h1bbdace_0
+  - lz4-c=1.9.3=h9c3ff4c_1
+  - markupsafe=2.1.0=py39hb9d737c_1
+  - matplotlib=3.5.1=py39hf3d152e_0
+  - matplotlib-base=3.5.1=py39h2fa2bec_0
+  - matplotlib-inline=0.1.3=pyhd8ed1ab_0
+  - mistune=0.8.4=py39h3811e60_1005
+  - munkres=1.1.4=pyh9f0ad1d_0
+  - mysql-common=8.0.28=ha770c72_0
+  - mysql-libs=8.0.28=hfa10184_0
+  - nbclient=0.5.12=pyhd8ed1ab_0
+  - nbconvert=6.4.2=py39hf3d152e_0
+  - nbformat=5.1.3=pyhd8ed1ab_0
+  - ncurses=6.3=h9c3ff4c_0
+  - nest-asyncio=1.5.4=pyhd8ed1ab_0
+  - notebook=6.4.8=pyha770c72_0
+  - nspr=4.32=h9c3ff4c_1
+  - nss=3.74=hb5efdd6_0
+  - numba=0.55.1=py39h56b8d98_0
+  - numpy=1.21.5=py39haac66dc_0
+  - openjpeg=2.4.0=hb52868f_1
+  - openssl=1.1.1l=h7f98852_0
+  - packaging=21.3=pyhd8ed1ab_0
+  - pandas=1.4.1=py39hde0f152_0
+  - pandoc=2.17.1.1=ha770c72_0
+  - pandocfilters=1.5.0=pyhd8ed1ab_0
+  - parso=0.8.3=pyhd8ed1ab_0
+  - pcre=8.45=h9c3ff4c_0
+  - pexpect=4.8.0=pyh9f0ad1d_2
+  - pickleshare=0.7.5=py_1003
+  - pillow=9.0.1=py39hae2aec6_2
+  - pip=22.0.4=pyhd8ed1ab_0
+  - prometheus_client=0.13.1=pyhd8ed1ab_0
+  - prompt-toolkit=3.0.27=pyha770c72_0
+  - prompt_toolkit=3.0.27=hd8ed1ab_0
+  - pthread-stubs=0.4=h36c2ea0_1001
+  - ptyprocess=0.7.0=pyhd3deb0d_0
+  - pure_eval=0.2.2=pyhd8ed1ab_0
+  - pycparser=2.21=pyhd8ed1ab_0
+  - pygments=2.11.2=pyhd8ed1ab_0
+  - pyparsing=3.0.7=pyhd8ed1ab_0
+  - pyqt=5.12.3=py39hf3d152e_8
+  - pyqt-impl=5.12.3=py39hde8b62d_8
+  - pyqt5-sip=4.19.18=py39he80948d_8
+  - pyqtchart=5.12=py39h0fcd23e_8
+  - pyqtwebengine=5.12.1=py39h0fcd23e_8
+  - pyrsistent=0.18.1=py39h3811e60_0
+  - python=3.9.10=h85951f9_2_cpython
+  - python-dateutil=2.8.2=pyhd8ed1ab_0
+  - python_abi=3.9=2_cp39
+  - pytz=2021.3=pyhd8ed1ab_0
+  - pyzmq=22.3.0=py39h37b5a0c_1
+  - qt=5.12.9=ha98a1a1_5
+  - qtconsole=5.2.2=pyhd8ed1ab_1
+  - qtconsole-base=5.2.2=pyhd8ed1ab_1
+  - qtpy=2.0.1=pyhd8ed1ab_0
+  - readline=8.1=h46c0cb4_0
+  - scipy=1.8.0=py39hee8e79c_1
+  - send2trash=1.8.0=pyhd8ed1ab_0
+  - setuptools=60.9.3=py39hf3d152e_0
+  - six=1.16.0=pyh6c4a22f_0
+  - sqlite=3.37.0=h9cd32fc_0
+  - stack_data=0.2.0=pyhd8ed1ab_0
+  - terminado=0.13.3=py39hf3d152e_0
+  - testpath=0.6.0=pyhd8ed1ab_0
+  - tk=8.6.12=h27826a3_0
+  - tornado=6.1=py39h3811e60_2
+  - traitlets=5.1.1=pyhd8ed1ab_0
+  - tzdata=2021e=he74cb21_0
+  - unicodedata2=14.0.0=py39h3811e60_0
+  - wcwidth=0.2.5=pyh9f0ad1d_2
+  - webencodings=0.5.1=py_1
+  - wheel=0.37.1=pyhd8ed1ab_0
+  - widgetsnbextension=3.5.2=py39hf3d152e_1
+  - xorg-libxau=1.0.9=h7f98852_0
+  - xorg-libxdmcp=1.1.3=h7f98852_0
+  - xz=5.2.5=h516909a_1
+  - zeromq=4.3.4=h9c3ff4c_1
+  - zipp=3.7.0=pyhd8ed1ab_1
+  - zlib=1.2.11=h36c2ea0_1013
+  - zstd=1.5.2=ha95c52a_0
   - pip:
-    - absl-py==0.9.0
-    - appdirs==1.4.3
-    - attrs==19.3.0
-    - bleach==3.1.0
-    - cachecontrol==0.12.6
-    - cachetools==4.1.0
-    - chardet==3.0.4
-    - cherrypy==3.2.4
-    - configparser==4.0.2
-    - cython==0.29.14
-    - defusedxml==0.6.0
-    - entrypoints==0.3
-    - fairseq==0.8.0
-    - fastbpe==0.1.0
+    - absl-py==1.0.0
+    - aiohttp==3.8.1
+    - aiosignal==1.2.0
+    - async-timeout==4.0.2
+    - cachetools==5.0.0
+    - charset-normalizer==2.0.12
+    - frozenlist==1.3.0
+    - fsspec==2022.2.0
     - future==0.18.2
-    - google-auth==1.16.1
-    - google-auth-oauthlib==0.4.1
-    - grpcio==1.29.0
-    - hdmedians==0.13
-    - idna==2.8
-    - ipykernel==5.1.3
-    - ipywidgets==7.5.1
-    - jinja2==2.10.3
-    - jsonschema==3.2.0
-    - jupyter==1.0.0
-    - jupyter-client==5.3.4
-    - jupyter-console==6.0.0
-    - jupyter-core==4.6.1
-    - llvmlite==0.31.0
-    - lockfile==0.12.2
-    - markdown==3.2.2
-    - markupsafe==1.1.1
-    - matplotlib==3.1.1
-    - mistune==0.8.4
-    - more-itertools==8.0.2
-    - msgpack==0.6.2
-    - natsort==6.2.0
-    - nbconvert==5.6.1
-    - nbformat==4.4.0
-    - notebook==6.0.2
-    - numba==0.47.0
-    - oauthlib==3.1.0
-    - packaging==20.1
-    - pandocfilters==1.4.2
-    - pluggy==0.13.1
-    - portalocker==1.5.1
-    - prometheus-client==0.7.1
-    - protobuf==3.12.2
-    - py==1.8.1
+    - google-auth==2.6.0
+    - google-auth-oauthlib==0.4.6
+    - grpcio==1.44.0
+    - idna==3.3
+    - iniconfig==1.1.1
+    - joblib==1.1.0
+    - markdown==3.3.6
+    - multidict==6.0.2
+    - oauthlib==3.2.0
+    - pluggy==1.0.0
+    - protobuf==3.19.4
+    - py==1.11.0
     - pyasn1==0.4.8
     - pyasn1-modules==0.2.8
-    - pyrsistent==0.15.6
-    - pytest==5.4.3
-    - pytorch-lightning==0.8.1
-    - pyyaml==5.3.1
-    - pyzmq==18.1.1
-    - qtconsole==4.6.0
-    - regex==2019.8.19
-    - requests==2.22.0
-    - requests-oauthlib==1.3.0
-    - rsa==4.0
-    - sacrebleu==1.4.2
-    - scikit-bio==0.5.5
-    - send2trash==1.5.0
-    - tensorboard==2.2.2
-    - tensorboard-plugin-wit==1.6.0.post3
-    - terminado==0.8.3
-    - testpath==0.4.4
-    - torch==1.4.0
-    - typing==3.7.4.1
-    - urllib3==1.25.7
-    - webencodings==0.5.1
-    - werkzeug==1.0.1
-    - widgetsnbextension==3.5.1
-
+    - pydeprecate==0.3.1
+    - pytest==7.0.1
+    - pytorch-lightning==1.5.8
+    - pyyaml==6.0
+    - requests==2.27.1
+    - requests-oauthlib==1.3.1
+    - rsa==4.8
+    - scikit-learn==1.0.2
+    - tensorboard==2.8.0
+    - tensorboard-data-server==0.6.1
+    - tensorboard-plugin-wit==1.8.1
+    - threadpoolctl==3.1.0
+    - tomli==2.0.1
+    - torch==1.10.2+cu113
+    - torchaudio==0.10.2+cu113
+    - torchmetrics==0.7.2
+    - torchvision==0.11.3+cu113
+    - tqdm==4.63.0
+    - typing-extensions==4.1.1
+    - urllib3==1.26.8
+    - werkzeug==2.0.3
+    - yarl==1.7.2
+prefix: /mnt/home/jmorton/miniconda3/envs/deepblast2

From e1cfd83e661a25f648c6309c68a5c1d41dc78c80 Mon Sep 17 00:00:00 2001
From: mortonjt <jamietmorton@gmail.com>
Date: Wed, 30 Mar 2022 21:05:22 -0400
Subject: [PATCH 2/3] adding backwards compatible fix to load models

---
 deepblast/trainer.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/deepblast/trainer.py b/deepblast/trainer.py
index 164c5f5..c2b8b0d 100644
--- a/deepblast/trainer.py
+++ b/deepblast/trainer.py
@@ -25,7 +25,11 @@ class LightningAligner(pl.LightningModule):
 
     def __init__(self, args):
         super(LightningAligner, self).__init__()
-        self._hparams = args
+        if isinstance(args, dict):
+            self._hparams = argparse.Namespace(**args)
+        else:
+            self._hparams = args
+
         self.tokenizer = UniprotTokenizer(pad_ends=False)
         #self.hparams = args
         self.initialize_aligner()

From b5bd93b93ac1d59222693a7c511b0ce41241d29e Mon Sep 17 00:00:00 2001
From: mortonjt <jamietmorton@gmail.com>
Date: Wed, 30 Mar 2022 21:07:30 -0400
Subject: [PATCH 3/3] updating ci

---
 ci/conda_requirements.yml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/ci/conda_requirements.yml b/ci/conda_requirements.yml
index 33ea240..ed404b7 100644
--- a/ci/conda_requirements.yml
+++ b/ci/conda_requirements.yml
@@ -1,6 +1,5 @@
 name: deepblast2
 channels:
-  - biobakery
   - conda-forge
   - bioconda
   - defaults
@@ -224,13 +223,12 @@ dependencies:
     - tensorboard-plugin-wit==1.8.1
     - threadpoolctl==3.1.0
     - tomli==2.0.1
-    - torch==1.10.2+cu113
-    - torchaudio==0.10.2+cu113
+    - torch==1.10.2
+    - torchaudio==0.10.2
     - torchmetrics==0.7.2
-    - torchvision==0.11.3+cu113
+    - torchvision==0.11.3
     - tqdm==4.63.0
     - typing-extensions==4.1.1
     - urllib3==1.26.8
     - werkzeug==2.0.3
     - yarl==1.7.2
-prefix: /mnt/home/jmorton/miniconda3/envs/deepblast2