Create env.yml (#6)
Browse files- Create env.yml (ddafadf5c8ea19fa70bf50f2f4122d1633d60956)
Co-authored-by: Ryan Keivanfar <[email protected]>
env.yml
ADDED
@@ -0,0 +1,345 @@
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1 |
+
name: tahoeformer_env
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2 |
+
channels:
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3 |
+
- pytorch
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4 |
+
- nvidia
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5 |
+
- bioconda
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6 |
+
- conda-forge
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7 |
+
dependencies:
|
8 |
+
- _openmp_mutex=4.5=3_kmp_llvm
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9 |
+
- alsa-lib=1.2.8=h166bdaf_0
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10 |
+
- argcomplete=3.6.2=pyhd8ed1ab_0
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11 |
+
- argh=0.31.3=pyhd8ed1ab_1
|
12 |
+
- asttokens=3.0.0=pyhd8ed1ab_1
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13 |
+
- attr=2.5.1=h166bdaf_1
|
14 |
+
- bcftools=1.17=h3cc50cf_1
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15 |
+
- biopython=1.85=py310ha75aee5_1
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16 |
+
- blas=1.0=mkl
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17 |
+
- brotli=1.1.0=hb9d3cd8_2
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18 |
+
- brotli-bin=1.1.0=hb9d3cd8_2
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19 |
+
- bzip2=1.0.8=h4bc722e_7
|
20 |
+
- c-ares=1.34.5=hb9d3cd8_0
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21 |
+
- ca-certificates=2025.4.26=hbd8a1cb_0
|
22 |
+
- cached-property=1.5.2=hd8ed1ab_1
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23 |
+
- cached_property=1.5.2=pyha770c72_1
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24 |
+
- cairo=1.16.0=ha61ee94_1014
|
25 |
+
- certifi=2025.4.26=pyhd8ed1ab_0
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26 |
+
- comm=0.2.2=pyhd8ed1ab_1
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27 |
+
- contourpy=1.3.2=py310h3788b33_0
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28 |
+
- cpython=3.10.17=py310hd8ed1ab_0
|
29 |
+
- cramjam=2.10.0=py310hed47299_0
|
30 |
+
- cuda-cudart=12.1.105=0
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31 |
+
- cuda-cupti=12.1.105=0
|
32 |
+
- cuda-libraries=12.1.0=0
|
33 |
+
- cuda-nvrtc=12.1.105=0
|
34 |
+
- cuda-nvtx=12.1.105=0
|
35 |
+
- cuda-opencl=12.9.19=0
|
36 |
+
- cuda-runtime=12.1.0=0
|
37 |
+
- cuda-version=12.9=3
|
38 |
+
- cudnn=9.9.0.52=h3828807_0
|
39 |
+
- cycler=0.12.1=pyhd8ed1ab_1
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40 |
+
- dbus=1.13.6=h5008d03_3
|
41 |
+
- debugpy=1.8.14=py310hf71b8c6_0
|
42 |
+
- decorator=5.2.1=pyhd8ed1ab_0
|
43 |
+
- exceptiongroup=1.2.2=pyhd8ed1ab_1
|
44 |
+
- executing=2.2.0=pyhd8ed1ab_0
|
45 |
+
- expat=2.7.0=h5888daf_0
|
46 |
+
- fastparquet=2024.11.0=py310hf462985_0
|
47 |
+
- fftw=3.3.10=nompi_hf1063bd_110
|
48 |
+
- filelock=3.18.0=pyhd8ed1ab_0
|
49 |
+
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
|
50 |
+
- font-ttf-inconsolata=3.000=h77eed37_0
|
51 |
+
- font-ttf-source-code-pro=2.038=h77eed37_0
|
52 |
+
- font-ttf-ubuntu=0.83=h77eed37_3
|
53 |
+
- fontconfig=2.14.2=h14ed4e7_0
|
54 |
+
- fonts-conda-ecosystem=1=0
|
55 |
+
- fonts-conda-forge=1=0
|
56 |
+
- fonttools=4.57.0=py310h89163eb_0
|
57 |
+
- freetype=2.12.1=h267a509_2
|
58 |
+
- fsspec=2025.3.2=pyhd8ed1ab_0
|
59 |
+
- gettext=0.24.1=h5888daf_0
|
60 |
+
- gettext-tools=0.24.1=h5888daf_0
|
61 |
+
- gffutils=0.13=pyh7cba7a3_0
|
62 |
+
- glib=2.80.2=hf974151_0
|
63 |
+
- glib-tools=2.80.2=hb6ce0ca_0
|
64 |
+
- gmp=6.3.0=hac33072_2
|
65 |
+
- gmpy2=2.2.1=py310he8512ff_0
|
66 |
+
- graphite2=1.3.13=h59595ed_1003
|
67 |
+
- gsl=2.7=he838d99_0
|
68 |
+
- gst-plugins-base=1.21.3=h4243ec0_1
|
69 |
+
- gstreamer=1.21.3=h25f0c4b_1
|
70 |
+
- gstreamer-orc=0.4.41=h17648ed_0
|
71 |
+
- h5py=3.9.0=nompi_py310h367e799_100
|
72 |
+
- harfbuzz=6.0.0=h8e241bc_0
|
73 |
+
- hdf5=1.14.0=nompi_h5231ba7_103
|
74 |
+
- htslib=1.17=h6bc39ce_1
|
75 |
+
- icu=70.1=h27087fc_0
|
76 |
+
- importlib-metadata=8.6.1=pyha770c72_0
|
77 |
+
- ipykernel=6.29.5=pyh3099207_0
|
78 |
+
- ipython=8.36.0=pyh907856f_0
|
79 |
+
- jack=1.9.22=h11f4161_0
|
80 |
+
- jedi=0.19.2=pyhd8ed1ab_1
|
81 |
+
- jinja2=3.1.6=pyhd8ed1ab_0
|
82 |
+
- joblib=1.5.0=pyhd8ed1ab_0
|
83 |
+
- jpeg=9e=h0b41bf4_3
|
84 |
+
- jupyter_client=8.6.3=pyhd8ed1ab_1
|
85 |
+
- jupyter_core=5.7.2=pyh31011fe_1
|
86 |
+
- keyutils=1.6.1=h166bdaf_0
|
87 |
+
- kiwisolver=1.4.7=py310h3788b33_0
|
88 |
+
- krb5=1.20.1=hf9c8cef_0
|
89 |
+
- lame=3.100=h166bdaf_1003
|
90 |
+
- lcms2=2.15=hfd0df8a_0
|
91 |
+
- ld_impl_linux-64=2.43=h712a8e2_4
|
92 |
+
- lerc=4.0.0=h0aef613_1
|
93 |
+
- libaec=1.1.3=h59595ed_0
|
94 |
+
- libasprintf=0.24.1=h8e693c7_0
|
95 |
+
- libasprintf-devel=0.24.1=h8e693c7_0
|
96 |
+
- libblas=3.9.0=16_linux64_mkl
|
97 |
+
- libbrotlicommon=1.1.0=hb9d3cd8_2
|
98 |
+
- libbrotlidec=1.1.0=hb9d3cd8_2
|
99 |
+
- libbrotlienc=1.1.0=hb9d3cd8_2
|
100 |
+
- libcap=2.66=ha37c62d_0
|
101 |
+
- libcblas=3.9.0=16_linux64_mkl
|
102 |
+
- libclang=15.0.7=default_h127d8a8_5
|
103 |
+
- libclang13=15.0.7=default_h5d6823c_5
|
104 |
+
- libcublas=12.1.0.26=0
|
105 |
+
- libcufft=11.0.2.4=0
|
106 |
+
- libcufile=1.14.0.30=4
|
107 |
+
- libcups=2.3.3=h36d4200_3
|
108 |
+
- libcurand=10.3.10.19=0
|
109 |
+
- libcurl=7.87.0=h6312ad2_0
|
110 |
+
- libcusolver=11.4.4.55=0
|
111 |
+
- libcusparse=12.0.2.55=0
|
112 |
+
- libdb=6.2.32=h9c3ff4c_0
|
113 |
+
- libdeflate=1.17=h0b41bf4_0
|
114 |
+
- libedit=3.1.20250104=pl5321h7949ede_0
|
115 |
+
- libev=4.33=hd590300_2
|
116 |
+
- libevent=2.1.10=h9b69904_4
|
117 |
+
- libexpat=2.7.0=h5888daf_0
|
118 |
+
- libffi=3.4.6=h2dba641_1
|
119 |
+
- libflac=1.4.3=h59595ed_0
|
120 |
+
- libgcc=14.2.0=h767d61c_2
|
121 |
+
- libgcc-ng=14.2.0=h69a702a_2
|
122 |
+
- libgcrypt=1.11.0=ha770c72_2
|
123 |
+
- libgcrypt-devel=1.11.0=hb9d3cd8_2
|
124 |
+
- libgcrypt-lib=1.11.0=hb9d3cd8_2
|
125 |
+
- libgcrypt-tools=1.11.0=hb9d3cd8_2
|
126 |
+
- libgettextpo=0.24.1=h5888daf_0
|
127 |
+
- libgettextpo-devel=0.24.1=h5888daf_0
|
128 |
+
- libgfortran=14.2.0=h69a702a_2
|
129 |
+
- libgfortran-ng=14.2.0=h69a702a_2
|
130 |
+
- libgfortran5=14.2.0=hf1ad2bd_2
|
131 |
+
- libglib=2.80.2=hf974151_0
|
132 |
+
- libgpg-error=1.55=h3f2d84a_0
|
133 |
+
- libhwloc=2.9.1=hd6dc26d_0
|
134 |
+
- libiconv=1.18=h4ce23a2_1
|
135 |
+
- liblapack=3.9.0=16_linux64_mkl
|
136 |
+
- libllvm15=15.0.7=hadd5161_1
|
137 |
+
- libltdl=2.4.3a=h5888daf_0
|
138 |
+
- libnghttp2=1.51.0=hdcd2b5c_0
|
139 |
+
- libnpp=12.0.2.50=0
|
140 |
+
- libnsl=2.0.1=hd590300_0
|
141 |
+
- libnvjitlink=12.1.105=0
|
142 |
+
- libnvjpeg=12.1.1.14=0
|
143 |
+
- libogg=1.3.5=hd0c01bc_1
|
144 |
+
- libopus=1.5.2=hd0c01bc_0
|
145 |
+
- libpng=1.6.43=h2797004_0
|
146 |
+
- libpq=15.1=h2baec63_3
|
147 |
+
- libsndfile=1.2.2=hc60ed4a_1
|
148 |
+
- libsodium=1.0.18=h36c2ea0_1
|
149 |
+
- libsqlite=3.46.0=hde9e2c9_0
|
150 |
+
- libssh2=1.10.0=haa6b8db_3
|
151 |
+
- libstdcxx=14.2.0=h8f9b012_2
|
152 |
+
- libstdcxx-ng=14.2.0=h4852527_2
|
153 |
+
- libsystemd0=252=h2a991cd_0
|
154 |
+
- libtiff=4.5.0=h6adf6a1_2
|
155 |
+
- libtool=2.5.4=h5888daf_0
|
156 |
+
- libudev1=253=h0b41bf4_0
|
157 |
+
- libuuid=2.38.1=h0b41bf4_0
|
158 |
+
- libvorbis=1.3.7=h9c3ff4c_0
|
159 |
+
- libwebp-base=1.5.0=h851e524_0
|
160 |
+
- libxcb=1.13=h7f98852_1004
|
161 |
+
- libxcrypt=4.4.36=hd590300_1
|
162 |
+
- libxkbcommon=1.5.0=h79f4944_1
|
163 |
+
- libxml2=2.10.3=hca2bb57_4
|
164 |
+
- libzlib=1.2.13=h4ab18f5_6
|
165 |
+
- llvm-openmp=15.0.7=h0cdce71_0
|
166 |
+
- lz4-c=1.9.4=hcb278e6_0
|
167 |
+
- markupsafe=3.0.2=py310h89163eb_1
|
168 |
+
- matplotlib=3.9.1=py310hff52083_1
|
169 |
+
- matplotlib-base=3.9.1=py310hf02ac8c_2
|
170 |
+
- matplotlib-inline=0.1.7=pyhd8ed1ab_1
|
171 |
+
- mkl=2022.2.1=h84fe81f_16997
|
172 |
+
- mpc=1.3.1=h24ddda3_1
|
173 |
+
- mpfr=4.2.1=h90cbb55_3
|
174 |
+
- mpg123=1.32.9=hc50e24c_0
|
175 |
+
- mpmath=1.3.0=pyhd8ed1ab_1
|
176 |
+
- munkres=1.1.4=pyh9f0ad1d_0
|
177 |
+
- mysql-common=8.0.32=h14678bc_0
|
178 |
+
- mysql-libs=8.0.32=h54cf53e_0
|
179 |
+
- ncurses=6.5=h2d0b736_3
|
180 |
+
- nest-asyncio=1.6.0=pyhd8ed1ab_1
|
181 |
+
- networkx=3.4.2=pyh267e887_2
|
182 |
+
- nspr=4.36=h5888daf_0
|
183 |
+
- nss=3.100=hca3bf56_0
|
184 |
+
- numpy=1.26.4=py310hb13e2d6_0
|
185 |
+
- ocl-icd=2.3.3=hb9d3cd8_0
|
186 |
+
- opencl-headers=2024.10.24=h5888daf_0
|
187 |
+
- openjpeg=2.5.0=hfec8fc6_2
|
188 |
+
- openssl=1.1.1w=hd590300_0
|
189 |
+
- pandas=2.2.3=py310h5eaa309_3
|
190 |
+
- parso=0.8.4=pyhd8ed1ab_1
|
191 |
+
- patsy=1.0.1=pyhd8ed1ab_1
|
192 |
+
- pcre2=10.43=hcad00b1_0
|
193 |
+
- perl=5.32.1=7_hd590300_perl5
|
194 |
+
- pexpect=4.9.0=pyhd8ed1ab_1
|
195 |
+
- pickleshare=0.7.5=pyhd8ed1ab_1004
|
196 |
+
- pillow=9.4.0=py310h023d228_1
|
197 |
+
- pip=25.1.1=pyh8b19718_0
|
198 |
+
- pixman=0.46.0=h29eaf8c_0
|
199 |
+
- platformdirs=4.3.7=pyh29332c3_0
|
200 |
+
- ply=3.11=pyhd8ed1ab_3
|
201 |
+
- prompt-toolkit=3.0.51=pyha770c72_0
|
202 |
+
- psutil=7.0.0=py310ha75aee5_0
|
203 |
+
- pthread-stubs=0.4=hb9d3cd8_1002
|
204 |
+
- ptyprocess=0.7.0=pyhd8ed1ab_1
|
205 |
+
- pulseaudio=16.1=h4ab2085_1
|
206 |
+
- pure_eval=0.2.3=pyhd8ed1ab_1
|
207 |
+
- pygments=2.19.1=pyhd8ed1ab_0
|
208 |
+
- pyparsing=3.2.3=pyhd8ed1ab_1
|
209 |
+
- pyqt=5.15.7=py310hab646b1_3
|
210 |
+
- pyqt5-sip=12.11.0=py310heca2aa9_3
|
211 |
+
- pysam=0.21.0=py310hff46b53_0
|
212 |
+
- python=3.10.8=h257c98d_0_cpython
|
213 |
+
- python-dateutil=2.9.0.post0=pyhff2d567_1
|
214 |
+
- python-tzdata=2025.2=pyhd8ed1ab_0
|
215 |
+
- python_abi=3.10=7_cp310
|
216 |
+
- pytorch=2.5.1=py3.10_cuda12.1_cudnn9.1.0_0
|
217 |
+
- pytorch-cuda=12.1=ha16c6d3_6
|
218 |
+
- pytorch-mutex=1.0=cuda
|
219 |
+
- pytz=2025.2=pyhd8ed1ab_0
|
220 |
+
- pyvcf3=1.0.3=pyhdfd78af_0
|
221 |
+
- pyyaml=6.0.2=py310h89163eb_2
|
222 |
+
- pyzmq=26.2.0=py310h71f11fc_1
|
223 |
+
- qhull=2020.2=h434a139_5
|
224 |
+
- qt-main=5.15.6=h18908ee_6
|
225 |
+
- readline=8.2=h8c095d6_2
|
226 |
+
- samtools=1.18=hd87286a_0
|
227 |
+
- scikit-learn=1.6.1=py310h27f47ee_0
|
228 |
+
- scipy=1.15.2=py310h1d65ade_0
|
229 |
+
- seaborn=0.13.2=hd8ed1ab_3
|
230 |
+
- seaborn-base=0.13.2=pyhd8ed1ab_3
|
231 |
+
- setuptools=80.1.0=pyhff2d567_0
|
232 |
+
- simplejson=3.20.1=py310ha75aee5_0
|
233 |
+
- sip=6.7.12=py310hc6cd4ac_0
|
234 |
+
- six=1.17.0=pyhd8ed1ab_0
|
235 |
+
- stack_data=0.6.3=pyhd8ed1ab_1
|
236 |
+
- statsmodels=0.14.4=py310hf462985_0
|
237 |
+
- tbb=2021.9.0=hf52228f_0
|
238 |
+
- threadpoolctl=3.6.0=pyhecae5ae_0
|
239 |
+
- tk=8.6.13=noxft_h4845f30_101
|
240 |
+
- toml=0.10.2=pyhd8ed1ab_1
|
241 |
+
- tomli=2.2.1=pyhd8ed1ab_1
|
242 |
+
- torchtriton=3.1.0=py310
|
243 |
+
- tornado=6.4.2=py310ha75aee5_0
|
244 |
+
- traitlets=5.14.3=pyhd8ed1ab_1
|
245 |
+
- typing_extensions=4.13.2=pyh29332c3_0
|
246 |
+
- tzdata=2025b=h78e105d_0
|
247 |
+
- unicodedata2=16.0.0=py310ha75aee5_0
|
248 |
+
- wcwidth=0.2.13=pyhd8ed1ab_1
|
249 |
+
- wheel=0.45.1=pyhd8ed1ab_1
|
250 |
+
- xcb-util=0.4.0=h516909a_0
|
251 |
+
- xcb-util-image=0.4.0=h166bdaf_0
|
252 |
+
- xcb-util-keysyms=0.4.0=h516909a_0
|
253 |
+
- xcb-util-renderutil=0.3.9=h166bdaf_0
|
254 |
+
- xcb-util-wm=0.4.1=h516909a_0
|
255 |
+
- xkeyboard-config=2.38=h0b41bf4_0
|
256 |
+
- xorg-kbproto=1.0.7=hb9d3cd8_1003
|
257 |
+
- xorg-libice=1.1.2=hb9d3cd8_0
|
258 |
+
- xorg-libsm=1.2.6=he73a12e_0
|
259 |
+
- xorg-libx11=1.8.4=h0b41bf4_0
|
260 |
+
- xorg-libxau=1.0.12=hb9d3cd8_0
|
261 |
+
- xorg-libxdmcp=1.1.5=hb9d3cd8_0
|
262 |
+
- xorg-libxext=1.3.4=h0b41bf4_2
|
263 |
+
- xorg-libxrender=0.9.10=h7f98852_1003
|
264 |
+
- xorg-renderproto=0.11.1=hb9d3cd8_1003
|
265 |
+
- xorg-xextproto=7.3.0=hb9d3cd8_1004
|
266 |
+
- xorg-xproto=7.0.31=hb9d3cd8_1008
|
267 |
+
- xz=5.2.6=h166bdaf_0
|
268 |
+
- yaml=0.2.5=h7f98852_2
|
269 |
+
- zeromq=4.3.5=h59595ed_1
|
270 |
+
- zipp=3.21.0=pyhd8ed1ab_1
|
271 |
+
- zlib=1.2.13=h4ab18f5_6
|
272 |
+
- zstd=1.5.6=ha6fb4c9_0
|
273 |
+
- pip:
|
274 |
+
- accelerate==1.6.0
|
275 |
+
- aiohappyeyeballs==2.6.1
|
276 |
+
- aiohttp==3.11.18
|
277 |
+
- aiosignal==1.3.2
|
278 |
+
- annotated-types==0.7.0
|
279 |
+
- arrow==1.3.0
|
280 |
+
- async-timeout==5.0.1
|
281 |
+
- attrs==21.4.0
|
282 |
+
- binaryornot==0.4.4
|
283 |
+
- chardet==5.2.0
|
284 |
+
- charset-normalizer==3.4.2
|
285 |
+
- click==8.1.8
|
286 |
+
- colorlog==6.9.0
|
287 |
+
- cookiecutter==2.6.0
|
288 |
+
- deprecation==2.1.0
|
289 |
+
- discrete-key-value-bottleneck-pytorch==0.1.1
|
290 |
+
- docker-pycreds==0.4.0
|
291 |
+
- einops==0.8.1
|
292 |
+
- einx==0.3.0
|
293 |
+
- enformer-pytorch==0.8.10
|
294 |
+
- frozendict==2.4.6
|
295 |
+
- frozenlist==1.6.0
|
296 |
+
- future==1.0.0
|
297 |
+
- gitdb==4.0.12
|
298 |
+
- gitpython==3.1.44
|
299 |
+
- huggingface-hub==0.30.2
|
300 |
+
- idna==3.10
|
301 |
+
- kipoi==0.8.6
|
302 |
+
- kipoi-conda==0.3.1
|
303 |
+
- kipoi-utils==0.7.7
|
304 |
+
- kipoiseq==0.7.1
|
305 |
+
- lightning==2.5.1.post0
|
306 |
+
- lightning-utilities==0.14.3
|
307 |
+
- markdown-it-py==3.0.0
|
308 |
+
- mdurl==0.1.2
|
309 |
+
- multidict==6.4.3
|
310 |
+
- natsort==8.4.0
|
311 |
+
- ncls==0.0.68
|
312 |
+
- packaging==24.2
|
313 |
+
- polars==1.29.0
|
314 |
+
- propcache==0.3.1
|
315 |
+
- protobuf==6.30.2
|
316 |
+
- pydantic==2.11.4
|
317 |
+
- pydantic-core==2.33.2
|
318 |
+
- pyfaidx==0.8.1.4
|
319 |
+
- pyranges==0.1.4
|
320 |
+
- python-slugify==8.0.4
|
321 |
+
- pytorch-lightning==2.5.1.post0
|
322 |
+
- rdkit-pypi==2022.9.5
|
323 |
+
- regex==2024.11.6
|
324 |
+
- related==0.7.3
|
325 |
+
- requests==2.32.3
|
326 |
+
- rich==14.0.0
|
327 |
+
- safetensors==0.5.3
|
328 |
+
- sentry-sdk==2.27.0
|
329 |
+
- setproctitle==1.3.6
|
330 |
+
- smmap==5.0.2
|
331 |
+
- sorted-nearest==0.0.39
|
332 |
+
- sympy==1.13.1
|
333 |
+
- tabulate==0.9.0
|
334 |
+
- text-unidecode==1.3
|
335 |
+
- tinydb==4.8.2
|
336 |
+
- tokenizers==0.21.1
|
337 |
+
- torchmetrics==1.7.1
|
338 |
+
- tqdm==4.67.1
|
339 |
+
- transformers==4.51.3
|
340 |
+
- types-python-dateutil==2.9.0.20241206
|
341 |
+
- typing-inspection==0.4.0
|
342 |
+
- urllib3==2.4.0
|
343 |
+
- vector-quantize-pytorch==1.22.16
|
344 |
+
- wandb==0.19.10
|
345 |
+
- yarl==1.20.0
|