Updated TensorFlow Requirements in OSL-Dynamics (#296)

* Updated installation instructions for new TensorFlow version for osl-dynamics. * Updated BMRC env.
OHBA-analysis · May 24, 2024 · 35801b9 · 35801b9
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diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -26,7 +26,7 @@
 author = 'OHBA Analysis Group'
 
 # The full version, including alpha/beta/rc tags
-release = '0.5.1'
+release = '0.7.0'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/envs/bmrc.yml b/envs/bmrc.yml
@@ -12,7 +12,7 @@ dependencies:
   - ca-certificates=2024.2.2=hbcca054_0
   - certifi=2024.2.2=pyhd8ed1ab_0
   - charset-normalizer=3.3.2=pyhd8ed1ab_0
-  - curl=8.7.1=hca28451_0
+  - curl=8.8.0=he654da7_0
   - double-conversion=3.2.0=h27087fc_1
   - eigen=3.4.0=h00ab1b0_0
   - elfutils=0.190=h924a536_1
@@ -21,59 +21,64 @@ dependencies:
   - 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=h77eed37_1
+  - font-ttf-ubuntu=0.83=h77eed37_2
   - fontconfig=2.14.2=h14ed4e7_0
   - fonts-conda-ecosystem=1=0
   - fonts-conda-forge=1=0
   - freetype=2.12.1=h267a509_2
-  - gettext=0.21.1=h27087fc_0
+  - gettext=0.22.5=h59595ed_2
+  - gettext-tools=0.22.5=h59595ed_2
   - gl2ps=1.4.2=h0708190_0
   - gmp=6.3.0=h59595ed_1
   - gnutls=3.7.9=hb077bed_0
   - hdf4=4.2.15=h9772cbc_5
   - hdf5=1.12.2=nompi_h4df4325_101
   - icu=73.2=h59595ed_0
-  - idna=3.6=pyhd8ed1ab_0
-  - imageio=2.34.0=pyh4b66e23_0
+  - idna=3.7=pyhd8ed1ab_0
+  - imageio=2.34.1=pyh4b66e23_0
   - jpeg=9e=h0b41bf4_3
   - jsoncpp=1.9.5=h4bd325d_1
   - keyutils=1.6.1=h166bdaf_0
   - krb5=1.21.2=h659d440_0
   - lame=3.100=h166bdaf_1003
   - lcms2=2.14=h6ed2654_0
-  - ld_impl_linux-64=2.40=h41732ed_0
+  - ld_impl_linux-64=2.40=h55db66e_0
   - lerc=4.0.0=h27087fc_0
   - libaec=1.1.3=h59595ed_0
-  - libarchive=3.7.2=h2aa1ff5_1
-  - libblas=3.9.0=21_linux64_openblas
-  - libcblas=3.9.0=21_linux64_openblas
-  - libcurl=8.7.1=hca28451_0
+  - libarchive=3.7.4=hfca40fe_0
+  - libasprintf=0.22.5=h661eb56_2
+  - libasprintf-devel=0.22.5=h661eb56_2
+  - libblas=3.9.0=22_linux64_openblas
+  - libcblas=3.9.0=22_linux64_openblas
+  - libcurl=8.8.0=hca28451_0
   - libdeflate=1.14=h166bdaf_0
   - libdrm=2.4.120=hd590300_0
   - libedit=3.1.20191231=he28a2e2_2
   - libev=4.33=hd590300_2
   - libexpat=2.6.2=h59595ed_0
   - libffi=3.4.2=h7f98852_5
-  - libgcc-ng=13.2.0=h807b86a_5
-  - libgfortran-ng=13.2.0=h69a702a_5
-  - libgfortran5=13.2.0=ha4646dd_5
-  - libgomp=13.2.0=h807b86a_5
-  - libhwloc=2.9.3=default_h554bfaf_1009
+  - libgcc-ng=13.2.0=h77fa898_7
+  - libgettextpo=0.22.5=h59595ed_2
+  - libgettextpo-devel=0.22.5=h59595ed_2
+  - libgfortran-ng=13.2.0=h69a702a_7
+  - libgfortran5=13.2.0=hca663fb_7
+  - libgomp=13.2.0=h77fa898_7
+  - libhwloc=2.10.0=default_h5622ce7_1001
   - libiconv=1.17=hd590300_2
   - libidn2=2.3.7=hd590300_0
-  - liblapack=3.9.0=21_linux64_openblas
+  - liblapack=3.9.0=22_linux64_openblas
   - libllvm16=16.0.6=hb3ce162_3
   - libmicrohttpd=1.0.1=h97afed2_0
   - libnetcdf=4.8.1=nompi_h261ec11_106
   - libnghttp2=1.58.0=h47da74e_1
   - libnsl=2.0.1=hd590300_0
   - libogg=1.3.4=h7f98852_1
-  - libopenblas=0.3.26=pthreads_h413a1c8_0
+  - libopenblas=0.3.27=pthreads_h413a1c8_0
   - libpciaccess=0.18=hd590300_0
   - libpng=1.6.43=h2797004_0
-  - libsqlite=3.45.2=h2797004_0
+  - libsqlite=3.45.3=h2797004_0
   - libssh2=1.11.0=h0841786_0
-  - libstdcxx-ng=13.2.0=h7e041cc_5
+  - libstdcxx-ng=13.2.0=hc0a3c3a_7
   - libtasn1=4.19.0=h166bdaf_0
   - libtheora=1.1.1=h7f98852_1005
   - libtiff=4.4.0=h82bc61c_5
@@ -82,25 +87,25 @@ dependencies:
   - libva=2.18.0=h0b41bf4_0
   - libvorbis=1.3.7=h9c3ff4c_0
   - libvpx=1.11.0=h9c3ff4c_3
-  - libwebp-base=1.3.2=hd590300_0
+  - libwebp-base=1.4.0=hd590300_0
   - libxcb=1.13=h7f98852_1004
-  - libxml2=2.12.6=h232c23b_1
+  - libxml2=2.12.7=hc051c1a_0
   - libzip=1.10.1=h2629f0a_3
   - libzlib=1.2.13=hd590300_5
   - loguru=0.7.2=py38h578d9bd_1
   - lz4-c=1.9.4=hcb278e6_0
-  - lzo=2.10=h516909a_1000
+  - lzo=2.10=hd590300_1001
   - mesalib=23.0.2=h3855f93_0
-  - ncurses=6.4.20240210=h59595ed_0
+  - ncurses=6.5=h59595ed_0
   - nettle=3.9.1=h7ab15ed_0
   - openh264=2.3.1=hcb278e6_2
   - openjpeg=2.5.0=h7d73246_1
-  - openssl=3.2.1=hd590300_1
+  - openssl=3.3.0=h4ab18f5_2
   - p11-kit=0.24.1=hc5aa10d_0
   - packaging=24.0=pyhd8ed1ab_0
   - pillow=9.2.0=py38h9eb91d8_3
   - pip=23.3.1=pyhd8ed1ab_0
-  - platformdirs=4.2.0=pyhd8ed1ab_0
+  - platformdirs=4.2.2=pyhd8ed1ab_0
   - pooch=1.8.1=pyhd8ed1ab_0
   - proj=9.0.1=h93bde94_1
   - pthread-stubs=0.4=h36c2ea0_1001
@@ -110,15 +115,15 @@ dependencies:
   - python_abi=3.8=4_cp38
   - pyvista=0.38.5=pyhd8ed1ab_0
   - readline=8.2=h8228510_1
-  - requests=2.31.0=pyhd8ed1ab_0
-  - scooby=0.9.2=pyhd8ed1ab_0
-  - setuptools=69.2.0=pyhd8ed1ab_0
-  - sqlite=3.45.2=h2c6b66d_0
+  - requests=2.32.2=pyhd8ed1ab_0
+  - scooby=0.10.0=pyhd8ed1ab_0
+  - setuptools=70.0.0=pyhd8ed1ab_0
+  - sqlite=3.45.3=h2c6b66d_0
   - svt-av1=1.4.1=hcb278e6_0
-  - tbb=2021.11.0=h00ab1b0_1
-  - tbb-devel=2021.11.0=h5ccd973_1
+  - tbb=2021.12.0=h297d8ca_1
+  - tbb-devel=2021.12.0=h7c56ddd_1
   - tk=8.6.13=noxft_h4845f30_101
-  - typing_extensions=4.10.0=pyha770c72_0
+  - typing_extensions=4.11.0=pyha770c72_0
   - urllib3=2.2.1=pyhd8ed1ab_0
   - utfcpp=4.0.5=ha770c72_0
   - vtk=9.1.0=osmesa_py38h68dc7f3_115
@@ -148,7 +153,7 @@ dependencies:
   - xorg-xproto=7.0.31=h7f98852_1007
   - xz=5.2.6=h166bdaf_0
   - zlib=1.2.13=hd590300_5
-  - zstd=1.5.5=hfc55251_0
+  - zstd=1.5.6=ha6fb4c9_0
   - pip:
     - alabaster==0.7.13
     - anamnesis==1.0.4
@@ -159,7 +164,7 @@ dependencies:
     - asttokens==2.4.1
     - async-lru==2.0.4
     - attrs==23.2.0
-    - babel==2.14.0
+    - babel==2.15.0
     - backcall==0.2.0
     - beautifulsoup4==4.12.3
     - bleach==6.1.0
@@ -178,23 +183,23 @@ dependencies:
     - dill==0.3.8
     - distributed==2023.3.2
     - docutils==0.20.1
-    - exceptiongroup==1.2.0
+    - exceptiongroup==1.2.1
     - executing==2.0.1
     - fastjsonschema==2.19.1
-    - fonttools==4.50.0
+    - fonttools==4.51.0
     - fqdn==1.5.1
     - fslpy==3.11.3
-    - fsspec==2024.3.1
+    - fsspec==2024.5.0
     - glmtools==0.2.1
     - h11==0.14.0
     - h5io==0.1.7
-    - h5py==3.10.0
+    - h5py==3.11.0
     - httpcore==1.0.5
     - httpx==0.27.0
     - imagesize==1.4.1
     - importlib-metadata==4.13.0
     - importlib-resources==6.4.0
-    - ipycanvas==0.13.1
+    - ipycanvas==0.13.2
     - ipyevents==2.0.1
     - ipykernel==6.29.4
     - ipympl==0.9.3
@@ -205,47 +210,47 @@ dependencies:
     - isoduration==20.11.0
     - jedi==0.19.1
     - jinja2==3.0.3
-    - joblib==1.3.2
-    - json5==0.9.24
+    - joblib==1.4.2
+    - json5==0.9.25
     - jsonpointer==2.4
-    - jsonschema==4.21.1
+    - jsonschema==4.22.0
     - jsonschema-specifications==2023.12.1
     - jupyter==1.0.0
     - jupyter-client==8.1.0
     - jupyter-console==6.6.3
     - jupyter-core==5.7.2
     - jupyter-events==0.10.0
-    - jupyter-lsp==2.2.4
-    - jupyter-server==2.13.0
+    - jupyter-lsp==2.2.5
+    - jupyter-server==2.14.0
     - jupyter-server-terminals==0.5.3
-    - jupyterlab==4.1.5
+    - jupyterlab==4.2.1
     - jupyterlab-pygments==0.3.0
-    - jupyterlab-server==2.25.4
+    - jupyterlab-server==2.27.2
     - jupyterlab-widgets==3.0.10
     - kiwisolver==1.4.5
     - linkify-it-py==2.0.3
     - llvmlite==0.41.1
     - locket==1.0.0
-    - lxml==5.2.0
+    - lxml==5.2.2
     - markdown==3.6
     - markdown-it-py==3.0.0
     - markupsafe==2.1.5
     - mat73==0.62
     - matplotlib==3.7.1
-    - matplotlib-inline==0.1.6
-    - mdit-py-plugins==0.4.0
+    - matplotlib-inline==0.1.7
+    - mdit-py-plugins==0.4.1
     - mdurl==0.1.2
     - mistune==3.0.2
     - mne==1.3.1
     - msgpack==1.0.8
     - nbclient==0.10.0
-    - nbconvert==7.16.3
-    - nbformat==5.10.3
+    - nbconvert==7.16.4
+    - nbformat==5.10.4
     - nest-asyncio==1.6.0
     - neurokit2==0.2.3
     - nibabel==5.1.0
     - nilearn==0.10.2
-    - notebook==7.1.2
+    - notebook==7.2.0
     - notebook-shim==0.2.4
     - numba==0.58.0
     - numpy==1.23.5
@@ -258,7 +263,7 @@ dependencies:
     - panel==1.2.3
     - param==2.1.0
     - parse==1.19.0
-    - parso==0.8.3
+    - parso==0.8.4
     - partd==1.4.1
     - pexpect==4.9.0
     - pickleshare==0.7.5
@@ -270,25 +275,25 @@ dependencies:
     - ptyprocess==0.7.0
     - pure-eval==0.2.2
     - pycparser==2.22
-    - pygments==2.17.2
+    - pygments==2.18.0
     - pyparsing==3.1.2
     - python-dateutil==2.9.0.post0
     - python-json-logger==2.0.7
     - pytz==2024.1
     - pyviz-comms==3.0.2
     - pyyaml==6.0.1
-    - pyzmq==25.1.2
-    - qtconsole==5.5.1
+    - pyzmq==26.0.3
+    - qtconsole==5.5.2
     - qtpy==2.4.1
-    - referencing==0.34.0
+    - referencing==0.35.1
     - rfc3339-validator==0.1.4
     - rfc3986-validator==0.1.1
-    - rpds-py==0.18.0
+    - rpds-py==0.18.1
     - sails==1.6.0
     - scikit-learn==1.3.1
     - scipy==1.10.1
     - seaborn==0.13.0
-    - send2trash==1.8.2
+    - send2trash==1.8.3
     - six==1.16.0
     - sniffio==1.3.1
     - snowballstemmer==2.2.0
@@ -307,21 +312,21 @@ dependencies:
     - tabulate==0.9.0
     - tblib==3.0.0
     - terminado==0.18.1
-    - threadpoolctl==3.4.0
-    - tinycss2==1.2.1
+    - threadpoolctl==3.5.0
+    - tinycss2==1.3.0
     - tomli==2.0.1
     - toolz==0.12.1
     - tornado==6.4
     - tqdm==4.66.1
-    - traitlets==5.14.2
+    - traitlets==5.14.3
     - types-python-dateutil==2.9.0.20240316
     - uc-micro-py==1.0.3
     - uri-template==1.3.0
     - wcwidth==0.2.13
     - webcolors==1.13
     - webencodings==0.5.1
-    - websocket-client==1.7.0
+    - websocket-client==1.8.0
     - widgetsnbextension==4.0.10
-    - xyzservices==2023.10.1
+    - xyzservices==2024.4.0
     - zict==3.0.0
-    - zipp==3.18.1
+    - zipp==3.18.2
diff --git a/envs/linux-full-with-spyder.yml b/envs/linux-full-with-spyder.yml
@@ -39,8 +39,8 @@ dependencies:
   - panel==1.2.3
   - pqdm==0.2.0
   - seaborn==0.13.0
-  - tensorflow==2.9.1
-  - tensorflow_probability==0.17.0
+  - tensorflow==2.11.0
+  - tensorflow_probability==0.19.0
   - tqdm==4.66.1
   - osfclient==0.0.5
   - osl

diff --git a/envs/linux-full.yml b/envs/linux-full.yml
@@ -38,8 +38,8 @@ dependencies:
   - panel==1.2.3
   - pqdm==0.2.0
   - seaborn==0.13.0
-  - tensorflow==2.9.1
-  - tensorflow_probability==0.17.0
+  - tensorflow==2.11.0
+  - tensorflow_probability==0.19.0
   - tqdm==4.66.1
   - osfclient==0.0.5
   - osl

diff --git a/envs/mac-full.yml b/envs/mac-full.yml
@@ -41,8 +41,8 @@ dependencies:
   - panel==1.2.3
   - pqdm==0.2.0
   - seaborn==0.13.0
-  - tensorflow-macos==2.9.1
-  - tensorflow_probability==0.17.0
+  - tensorflow-macos==2.11.0
+  - tensorflow_probability==0.19.0
   - tqdm==4.66.1
   - osfclient==0.0.5
   - osl