bella-companion 0.0.29__py3-none-any.whl → 0.0.32__py3-none-any.whl

bella_companion/simulations/beast_configs/fbd-2traits/Nonparametric.xml

@@ -1,70 +0,0 @@
-<?xml version="1.0"?>
-<beast
-    namespace="
-        :beast.base.evolution.operator.kernel
-        :beast.base.inference.parameter
-        :beast.base.inference.operator.kernel
-        :beast.base.inference
-        :beast.base.inference.distribution
-        :bdmmprime.distribution
-        :bdmmprime.parameterization
-        :feast.fileio
-        :feast.function
-        :feast.expressions"
-    version="2.5"
->
-    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
-
-    <map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
-    <map name="TaxonSetFromTree">feast.fileio.TaxonSetFromTree</map>
-	<map name="TraitSetFromTaxonSet">feast.fileio.TraitSetFromTaxonSet</map>
-    <map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
-
-    <TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
-    <TaxonSetFromTree id="taxonSet" tree="@tree"/>
-	<TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
-	<TypeSet id="typeSet" value="$(types)" typeTraitSet="@typeTraitSet"/>
-
-    <Uniform id="birthRatePrior" upper="$(birthRateUpper)"/>
-    <Uniform id="deathRatePrior" upper="$(deathRateUpper)"/>
-
-    <run spec="MCMC" chainLength="10000000">
-        <state id="state">
-            <stateNode spec="RealParameter" id="birthRate" value="$(birthRateInit)"/>
-            <stateNode spec="RealParameter" id="deathRate" value="$(deathRateInit)"/>
-        </state>
-
-        <distribution id="posterior" spec="CompoundDistribution">
-            <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution spec="BirthDeathMigrationDistribution" tree="@tree" typeTraitSet="@typeTraitSet">
-                    <parameterization spec="CanonicalParameterization" processLength="$(processLength)" typeSet="@typeSet">
-                        <birthRate id="birthRateSP" spec="SkylineVectorParameter" skylineValues="@birthRate" changeTimes="$(changeTimes)" typeSet="@typeSet"/>
-                        <deathRate id="deathRateSP" spec="SkylineVectorParameter" skylineValues="@deathRate" changeTimes="$(changeTimes)" typeSet="@typeSet"/>
-                        <migrationRate spec="SkylineMatrixParameter" skylineValues="$(migrationRate)" typeSet="@typeSet"/>
-                        <samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)" typeSet="@typeSet"/>
-                        <removalProb spec="SkylineVectorParameter" skylineValues="0.0" typeSet="@typeSet"/>
-                        <rhoSampling spec="TimedParameter" values="1" times="$(processLength)" typeSet="@typeSet"/>
-                    </parameterization>
-                    <startTypePriorProbs spec="RealParameter" value="$(startTypePriorProbs)"/>
-                </distribution>
-            </distribution>
-
-            <distribution id="prior" spec="CompoundDistribution">
-                <distribution spec="Prior" x="@deathRate" distr="@deathRatePrior"/>
-                <distribution spec="Prior" x="@birthRate" distr="@birthRatePrior"/>
-            </distribution>
-        </distribution>
-
-        <operator spec="BactrianScaleOperator" parameter="@birthRate" weight="30.0"/>
-        <operator spec="BactrianScaleOperator" parameter="@deathRate" weight="30.0"/>
-
-        <logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
-            <log idref="posterior"/>
-            <log idref="prior"/>
-            <log idref="likelihood"/>
-            <log idref="birthRateSP"/>
-            <log idref="deathRateSP"/>
-        </logger>
-    </run>
-
-</beast>

bella_companion/simulations/beast_configs/fbd-no-traits/GLM.xml

@@ -1,88 +0,0 @@
-<?xml version="1.0"?>
-<beast
-    namespace="
-        :beast.base.evolution.operator.kernel
-        :beast.base.inference.parameter
-        :beast.base.inference.operator.kernel
-        :beast.base.inference
-        :beast.base.inference.distribution
-        :bdmmprime.distribution
-        :bdmmprime.parameterization
-        :feast.fileio
-        :feast.function
-        :feast.expressions"
-    version="2.5"
->
-    <map name="Normal">beast.base.inference.distribution.Normal</map>
-    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
-
-    <map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
-
-    <TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
-
-    <Normal id="weightsPrior" mean="0" sigma="1"/>
-    <Uniform id="birthRatePrior" upper="$(birthRateUpper)"/>
-    <Uniform id="deathRatePrior" upper="$(deathRateUpper)"/>
-
-    <run spec="MCMC" chainLength="10000000">
-        <state id="state">
-            <stateNode spec="RealParameter" id="birthRateScaler" value="1"/>
-            <stateNode spec="RealParameter" id="deathRateScaler" value="1"/>
-            <stateNode spec="RealParameter" id="birthRateW" value="0"/>
-            <stateNode spec="RealParameter" id="deathRateW" value="0"/>
-        </state>
-
-        <distribution id="posterior" spec="CompoundDistribution">
-            <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution spec="BirthDeathMigrationDistribution" tree="@tree">
-                    <parameterization spec="CanonicalParameterization" processLength="$(processLength)">
-                        <birthRate id="birthRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)">
-                            <skylineValues id="birthRate" spec="glmprior.util.GLMLogLinear" coefficients="@birthRateW" scaleFactor="@birthRateScaler" transform="false">
-                                <predictor spec="RealParameter" value="$(timePredictor)"/>
-                                <predictor spec="RealParameter" value="$(randomPredictor)"/>
-                                <indicators spec="BooleanParameter" value="1"/>
-                            </skylineValues>
-                        </birthRate>
-                        <deathRate id="deathRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)">
-                            <skylineValues id="deathRate" spec="glmprior.util.GLMLogLinear" coefficients="@deathRateW" scaleFactor="@deathRateScaler" transform="false">
-                                <predictor spec="RealParameter" value="$(timePredictor)"/>
-                                <predictor spec="RealParameter" value="$(randomPredictor)"/>
-                                <indicators spec="BooleanParameter" value="1"/>
-                            </skylineValues>
-                        </deathRate>
-                        <samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)"/>
-                        <removalProb spec="SkylineVectorParameter" skylineValues="0.0"/>
-                        <rhoSampling spec="TimedParameter" values="1" times="$(processLength)"/>
-                    </parameterization>
-                </distribution>
-            </distribution>
-
-            <distribution id="prior" spec="CompoundDistribution">
-                <distribution spec="Prior" x="@birthRateScaler" distr="@weightsPrior"/>
-                <distribution spec="Prior" x="@deathRateScaler" distr="@weightsPrior"/>
-                <distribution spec="Prior" x="@birthRateW" distr="@weightsPrior"/>
-                <distribution spec="Prior" x="@deathRateW" distr="@weightsPrior"/>
-                <distribution spec="Prior" x="@birthRate" distr="@birthRatePrior"/>
-                <distribution spec="Prior" x="@deathRate" distr="@deathRatePrior"/>
-            </distribution>
-        </distribution>
-
-        <operator spec="BactrianScaleOperator" parameter="@birthRateScaler" weight="30.0"/>
-        <operator spec="BactrianScaleOperator" parameter="@deathRateScaler" weight="30.0"/>
-        <operator spec="BactrianRandomWalkOperator" parameter="@birthRateW" weight="30.0"/>
-        <operator spec="BactrianRandomWalkOperator" parameter="@deathRateW" weight="30.0"/>
-
-        <logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
-            <log idref="posterior"/>
-            <log idref="prior"/>
-            <log idref="likelihood"/>
-            <log idref="birthRateSP"/>
-            <log idref="deathRateSP"/>
-            <log idref="birthRateW"/>
-            <log idref="deathRateW"/>
-            <log idref="birthRateScaler"/>
-            <log idref="deathRateScaler"/>
-        </logger>
-    </run>
-
-</beast>

bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml

@@ -1,86 +0,0 @@
-<?xml version="1.0"?>
-<beast
-    namespace="
-        :beast.base.inference.parameter
-        :beast.base.inference.operator.kernel
-        :beast.base.inference
-        :beast.base.inference.distribution
-        :bdmmprime.distribution
-        :bdmmprime.parameterization
-        :feast.fileio
-        :feast.function
-        :feast.expressions"
-    version="2.5"
->
-    <map name="Normal">beast.base.inference.distribution.Normal</map>
-
-    <map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
-
-    <TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
-
-    <Normal id="weightsPrior" mean="0" sigma="1"/>
-
-    <run spec="MCMC" chainLength="10000000">
-        <state id="state">
-            <plate var="n" range="$(layersRange)">
-                <stateNode spec="RealParameter" id="birthRateW$(n)" value="0"/>
-                <stateNode spec="RealParameter" id="deathRateW$(n)" value="0"/>
-            </plate>
-        </state>
-
-        <distribution id="posterior" spec="CompoundDistribution">
-            <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution spec="BirthDeathMigrationDistribution" tree="@tree">
-                    <parameterization spec="CanonicalParameterization" processLength="$(processLength)">
-                        <birthRate id="birthRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)">
-                            <skylineValues id="birthRate" spec="bella.BayesMLP" nodes="$(nodes)">
-                                <predictor spec="RealParameter" value="$(timePredictor)"/>
-                                <predictor spec="RealParameter" value="$(randomPredictor)"/>
-                                <plate var="n" range="$(layersRange)">
-                                    <weights idref="birthRateW$(n)"/>
-                                </plate>
-                                <activationFunctionsOutput spec="bella.Sigmoid" upper="$(birthRateUpper)"/>
-                            </skylineValues>
-                        </birthRate>
-                        <deathRate id="deathRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)">
-                            <skylineValues id="deathRate" spec="bella.BayesMLP" nodes="$(nodes)">
-                                <predictor spec="RealParameter" value="$(timePredictor)"/>
-                                <predictor spec="RealParameter" value="$(randomPredictor)"/>
-                                <plate var="n" range="$(layersRange)">
-                                    <weights idref="deathRateW$(n)"/>
-                                </plate>
-                                <activationFunctionsOutput spec="bella.Sigmoid" upper="$(deathRateUpper)"/>
-                            </skylineValues>
-                        </deathRate>
-                        <samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)"/>
-                        <removalProb spec="SkylineVectorParameter" skylineValues="0.0"/>
-                        <rhoSampling spec="TimedParameter" values="1" times="$(processLength)"/>
-                    </parameterization>
-                </distribution>
-            </distribution>
-
-            <distribution id="prior" spec="CompoundDistribution">
-                <plate var="n" range="$(layersRange)">
-                    <distribution spec="Prior" x="@birthRateW$(n)" distr="@weightsPrior"/>
-                    <distribution spec="Prior" x="@deathRateW$(n)" distr="@weightsPrior"/>
-                </plate>
-            </distribution>
-        </distribution>
-
-        <plate var="n" range="$(layersRange)">
-            <operator spec="BactrianRandomWalkOperator" parameter="@birthRateW$(n)" weight="30.0"/>
-            <operator spec="BactrianRandomWalkOperator" parameter="@deathRateW$(n)" weight="30.0"/>
-        </plate>
-
-        <logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
-            <log idref="posterior"/>
-            <log idref="prior"/>
-            <log idref="likelihood"/>
-            <log idref="birthRateSP"/>
-            <log idref="deathRateSP"/>
-            <log idref="birthRate"/>
-            <log idref="deathRate"/>
-        </logger>
-    </run>
-
-</beast>

bella_companion/simulations/beast_configs/fbd-no-traits/Nonparametric.xml

@@ -1,62 +0,0 @@
-<?xml version="1.0"?>
-<beast
-    namespace="
-        :beast.base.evolution.operator.kernel
-        :beast.base.inference.parameter
-        :beast.base.inference.operator.kernel
-        :beast.base.inference
-        :beast.base.inference.distribution
-        :bdmmprime.distribution
-        :bdmmprime.parameterization
-        :feast.fileio
-        :feast.function
-        :feast.expressions"
-    version="2.5"
->
-    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
-
-    <map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
-
-    <TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
-
-    <Uniform id="birthRatePrior" upper="$(birthRateUpper)"/>
-    <Uniform id="deathRatePrior" upper="$(deathRateUpper)"/>
-
-    <run spec="MCMC" chainLength="10000000">
-        <state id="state">
-            <stateNode spec="RealParameter" id="birthRate" value="$(birthRateInit)"/>
-            <stateNode spec="RealParameter" id="deathRate" value="$(deathRateInit)"/>
-        </state>
-
-        <distribution id="posterior" spec="CompoundDistribution">
-            <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution spec="BirthDeathMigrationDistribution" tree="@tree">
-                    <parameterization spec="CanonicalParameterization" processLength="$(processLength)">
-                        <birthRate id="birthRateSP" spec="SkylineVectorParameter" skylineValues="@birthRate" changeTimes="$(changeTimes)"/>
-                        <deathRate id="deathRateSP" spec="SkylineVectorParameter" skylineValues="@deathRate" changeTimes="$(changeTimes)"/>
-                        <samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)"/>
-                        <removalProb spec="SkylineVectorParameter" skylineValues="0.0"/>
-                        <rhoSampling spec="TimedParameter" values="1" times="$(processLength)"/>
-                    </parameterization>
-                </distribution>
-            </distribution>
-
-            <distribution id="prior" spec="CompoundDistribution">
-                <distribution spec="Prior" x="@birthRate" distr="@birthRatePrior"/>
-                <distribution spec="Prior" x="@deathRate" distr="@deathRatePrior"/>
-            </distribution>
-        </distribution>
-
-        <operator spec="BactrianScaleOperator" parameter="@birthRate" weight="30.0"/>
-        <operator spec="BactrianScaleOperator" parameter="@deathRate" weight="30.0"/>
-
-        <logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
-            <log idref="posterior"/>
-            <log idref="prior"/>
-            <log idref="likelihood"/>
-            <log idref="birthRateSP"/>
-            <log idref="deathRateSP"/>
-        </logger>
-    </run>
-
-</beast>

bella_companion-0.0.29.dist-info/METADATA

@@ -1,16 +0,0 @@
-Metadata-Version: 2.1
-Name: bella-companion
-Version: 0.0.29
-Summary: 
-Author: gabriele-marino
-Author-email: gabmarino.8601@gmail.com
-Requires-Python: >=3.10,<4.0
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Requires-Dist: arviz (>=0.22.0,<0.23.0)
-Requires-Dist: bella-lumiere (>=0.0.14,<0.0.15)
-Requires-Dist: dotenv (>=0.9.9,<0.10.0)
-Requires-Dist: phylogenie (>=3.1.2,<4.0.0)
-Requires-Dist: seaborn (>=0.13.2,<0.14.0)

bella_companion-0.0.29.dist-info/RECORD

@@ -1,75 +0,0 @@
-bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bella_companion/cli.py,sha256=0SwDxkDPqvsp36kGnrBMLPIhAQM8PIpNXrztZayqmDc,2409
-bella_companion/eucovid/__init__.py,sha256=09Ld_G7fZvCDCgEWsmaOyLVQ8pFc9QHAGnXKJ9Zm2AM,81
-bella_companion/eucovid/beast_configs/GLM.xml,sha256=_pqs2-ADRGSmaBxCmMepuVMWiNEyce3azgE-qD6FNrs,10828
-bella_companion/eucovid/beast_configs/MLP.xml,sha256=M0_B6t0bZpjCAQqAmjrFshW96pt9sNREcoLUjwchX6Q,10616
-bella_companion/eucovid/beast_configs/Nonparametric.xml,sha256=n-t4sUfDS9AzC02tbIk5mx_RDg2l62ELhdR3I3_jjHE,17783
-bella_companion/eucovid/data/case_data.tsv,sha256=XaSzZh5NcEMVt9d_XlQ19T8UuEkHGrjpSFXhe9IycNg,12412
-bella_companion/eucovid/data/change_dates.tsv,sha256=_pmVFYiL4X9Pd79uYVgyz3sKeRap7xVcXk0OjqVhuVQ,227
-bella_companion/eucovid/data/msa.fasta,sha256=sWaVSINSJDDLjmwlpl31JWM5VnKF7yViSpERI69glQc,4839354
-bella_companion/eucovid/data/osi.tsv,sha256=iTDWL_-PnVQPg_-hWROXWKNFakDq_S1fEig1A_MqMVI,9228
-bella_companion/eucovid/data/predictors/all/closedborders_7e_nt.tsv,sha256=5gP-cEzgKSCvlK0_PlkrimYGEwOaLPO0GiiM4PIKU-M,280
-bella_companion/eucovid/data/predictors/all/dist_7e_ls.tsv,sha256=rr71QPiJu35CYbySMJyH_GDX51D2iTIncZImwAXIvlo,1890
-bella_companion/eucovid/data/predictors/all/flight_7e_ls.tsv,sha256=5WztZpQrjK7puERA1oxsCn5t2G1w9NGTGKjr85gMQ54,1873
-bella_companion/eucovid/data/predictors/all/flight_pop_x_7e_ls.tsv,sha256=qfRTXyZItzEm8pxurhFYO-DvpJXD-J4lMH5eyZKF0aE,1862
-bella_companion/eucovid/data/predictors/all/osi_x_7e_ls.tsv,sha256=kke2eHlVuc84qMj1WBllhBG2BQt7JHUWDZeiVoAP8Lw,1900
-bella_companion/eucovid/data/predictors/all/osi_y_7e_ls.tsv,sha256=5YDXe4GstyyRKP15213cAAEm5lVFW_bC98R8ipc1XoE,1900
-bella_companion/eucovid/data/predictors/all/pop_x_7e_ls.tsv,sha256=3fVYRQ1ylwsa7YptMU8f_xELwwqIF3Ux8akL9UaXKis,1904
-bella_companion/eucovid/data/predictors/all/pop_y_7e_ls.tsv,sha256=Ku39Ts0HW9r5lThAZ01V7HJDi0aoRYs0aQs5EXlZCkQ,1904
-bella_companion/eucovid/data/predictors/all/sharedborders_7e_nt.tsv,sha256=pPVT5DIaZuc3B0mSs-B3kw3G2zja1LfmL_xLwlNtLDo,280
-bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv,sha256=hH0xXD2lr_8RPQRqvENv6clPHauAXH22SGQHb3hlfzs,120
-bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv,sha256=XEepIXKRwcKknJq4-ovKlorvCypGi67B8znuQ5f1LTg,60
-bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv,sha256=tMR9-tuGtC3rVABXUtNdV9irUX-9aCCVb_fwksHTn8U,1068
-bella_companion/eucovid/run_beast.py,sha256=DU3T0xVVQ6y0ZClyFyouMd939V7sf5KGfadEzTDQf6I,3712
-bella_companion/platyrrhine/__init__.py,sha256=dIx6exNz-vuKiG5FZumvq74QUWcIEFd3L6ErqnOa83c,274
-bella_companion/platyrrhine/beast_config.xml,sha256=bLzavt-Zd8cmSgQQnlCBfZ9KyM7d1inOGx12VNjPFb4,7056
-bella_companion/platyrrhine/data/change_times.csv,sha256=tedobHbaY7-6M3V6F6HSqGAU9dpeeajR5mu1XGJfp6w,68
-bella_companion/platyrrhine/data/traits.csv,sha256=N_mCnaM9Gy0Qot7-l_mK0vMvr7e_5BZ4bgUHpcoG9UM,3949
-bella_companion/platyrrhine/data/trees.nwk,sha256=lpSiGUG5s3zE--IKPOyWrJ5vpJb_xAPnfxychs3YNIs,488232
-bella_companion/platyrrhine/results.py,sha256=qosxqstTy7uadHARRt1WqmxZzxnQ3hiTjtw6V-YWKGA,2556
-bella_companion/platyrrhine/run_beast.py,sha256=fnUmpJue3o0vZn9GWmwlmV0z2HIzXc4t_U2LFIKOq_I,2621
-bella_companion/platyrrhine/summarize_logs.py,sha256=82N7rcmLthCyQqmP4Yub4KUsIjNzQl9vEuFLMvIv03o,951
-bella_companion/simulations/__init__.py,sha256=ShYRdp1iSjnS_SzcsH-8jbqXz6P1nyRQZqAtPZJCMVE,454
-bella_companion/simulations/beast_configs/epi-multitype/GLM.xml,sha256=VymAYsaZVuB3EPE0DCQSXpKepVq8pPjKaB5yhEpaVkE,4334
-bella_companion/simulations/beast_configs/epi-multitype/MLP.xml,sha256=AoJyjvVcwKtut64d7sB2gnnenx5sXyuTTNCivykUyqU,4077
-bella_companion/simulations/beast_configs/epi-multitype/Nonparametric.xml,sha256=DfCMcLM53b-XP9oIiQ9wJWOVTEP3GnoZaL5BMzLLfIQ,3208
-bella_companion/simulations/beast_configs/epi-skyline/GLM.xml,sha256=7LtJhU7o7aQsnWK7ZIKj-mzmHgCn_RjxvKKbLIlp1Go,3619
-bella_companion/simulations/beast_configs/epi-skyline/MLP.xml,sha256=ptoLM0FLDp54bUSxPm12qIvOYWyBkWR1e9VWVWjgU8E,3426
-bella_companion/simulations/beast_configs/epi-skyline/Nonparametric.xml,sha256=LTiatqeAMiFfdD1leQ5TrGaJhsYwlkbMDpxqhVFOgUQ,2561
-bella_companion/simulations/beast_configs/fbd-2traits/GLM.xml,sha256=Iff0eAShKLeOnlTmNu6044Wljtla3yckqo2LZ7mP6LY,5897
-bella_companion/simulations/beast_configs/fbd-2traits/MLP.xml,sha256=RvF70fcnvoBcJxjyT4nELlFm94atSZpKm9d1aS-cJZ4,5428
-bella_companion/simulations/beast_configs/fbd-2traits/Nonparametric.xml,sha256=ev6ZfMeCwMyK54G_4O8g-tbgoxoD3asxt71x91Cb1QY,3618
-bella_companion/simulations/beast_configs/fbd-no-traits/GLM.xml,sha256=Caq7Gxqx-wYAu3_YkMikVqni3DjBv1Wt00sc1Upo1X8,4743
-bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml,sha256=JE_cGh2DW5yPAXyXXr0D3DlovmV-aIbze7qrhENHK3w,4275
-bella_companion/simulations/beast_configs/fbd-no-traits/Nonparametric.xml,sha256=m2xaHZwskCFInvVY1QH1fwQqH6p_fgESlPX2BbBeUhk,2822
-bella_companion/simulations/features.py,sha256=DZOBpJGlQ0UinqUZYbEtoemZ2eQGVLV_i-DfpW31qJI,104
-bella_companion/simulations/figures/__init__.py,sha256=aBYbJntH4egFmkSSWiVMYDEApXPYxJD7eA3TCPNNegM,658
-bella_companion/simulations/figures/epi_multitype_results.py,sha256=j85WgvN5AyAtX-CalMegr2lwlAZBmzyJxkikBPXRjCc,2629
-bella_companion/simulations/figures/epi_skyline_results.py,sha256=gI5Ha-OIEShcZLmqVuy0W8hJzkrsydQE-Coa65_BFCo,1667
-bella_companion/simulations/figures/explain/__init__.py,sha256=DnmVIWO65nTT5VsWnbS7NyYgKEY_eo4oMCtCY_ML2Vk,260
-bella_companion/simulations/figures/explain/pdp.py,sha256=3n3ssgufW_43pn2hO5V5J_jgcJH3Fpb8stIRtTnlQ8w,3801
-bella_companion/simulations/figures/explain/shap.py,sha256=qRfOMNwkU-hsBy5MHMTfVFAszaPESVOugCKQTVY8Q4Y,1940
-bella_companion/simulations/figures/fbd_2traits_results.py,sha256=JiXrbYkH1HwdJQhTHXj6KhMEXYgQmQ6LmDboAIO1CPA,2728
-bella_companion/simulations/figures/fbd_no_traits_results.py,sha256=fLsgpV3IbLLtxQEFNOL9K4jEEJrG324ziUM0rxIv7_k,1962
-bella_companion/simulations/figures/scenarios.py,sha256=gbMz1TUxxT2RSIq2kQlFioNdgSHk-gQY2OQuf6-7Fww,2817
-bella_companion/simulations/figures/utils.py,sha256=0M5OrxaEuqcj9rR2uAc_O7utQvhEceZGH0sKrGRWaWs,3129
-bella_companion/simulations/generate_data.py,sha256=edfhXrs76hl30i_xizup4z6qgzXZyaDzX_PVC62Ytpw,849
-bella_companion/simulations/generate_figures.py,sha256=layMgoj3Bfl78Ceb1oE7YirAQ8zhjDyD9IrxDRXf6go,657
-bella_companion/simulations/metrics.py,sha256=duIkPb8cCXmIzjKA2yk9HLf4Y9eFIB_hRWaH05uIDws,1876
-bella_companion/simulations/run_beast.py,sha256=qniy326i-vDCeHzzHpQRrSnY2ULqNNrO0z3GEsWx4Mc,3208
-bella_companion/simulations/scenarios/__init__.py,sha256=3Kl1lKcFpfb3vLX64DmSW4XCF5kXU1ZoHtstFH-ZIzU,876
-bella_companion/simulations/scenarios/common.py,sha256=_ddaSuTvEVdttGkXB4HPc2B7IB1F_GBOCW3cVOPZ-ZM,807
-bella_companion/simulations/scenarios/epi_multitype.py,sha256=fTkFeGHxyV_1f2nX3g_Oyr_e6wkorhXEicJjIAgeZKA,2439
-bella_companion/simulations/scenarios/epi_skyline.py,sha256=JqnOVATECxBUqEbkR5lBlMI2O8k4hO6ipR8k9cHUsm0,2365
-bella_companion/simulations/scenarios/fbd_2traits.py,sha256=-amB3NX0GsVgYbFuHH71t93FuXUEnRUyhWf2Qpcpia4,3541
-bella_companion/simulations/scenarios/fbd_no_traits.py,sha256=R6CH0fVeQg-Iesl39pq2uY8ICVEO4VZbvUVUCGwauJU,2520
-bella_companion/simulations/scenarios/scenario.py,sha256=_FRWAyOFbw94lAzd3zCD-1ek4TrssoiXfXRQPShLiIA,620
-bella_companion/simulations/summarize_logs.py,sha256=Shf3Dx9k4lTbmO__MSLw-aIA8a8kTCXhbctBcV6Izug,1216
-bella_companion/utils/__init__.py,sha256=UtMwPK9dWf9NAl0ic8CSsgdW7aSm-5J49OqgvD7UpYw,480
-bella_companion/utils/beast.py,sha256=TBa0cLklX1_tXqoQE4LRYvds7mLg_9fS2-6U6OHENHo,2184
-bella_companion/utils/explain.py,sha256=uP7HPyn2YiykAI69BQV3RooDpC6qKoCLXfp3Uibp4zk,1475
-bella_companion/utils/slurm.py,sha256=xEyf-Jxk8fy71t3fko_Ic9WtUFSdLFE3w4tR17gaBPw,1868
-bella_companion-0.0.29.dist-info/METADATA,sha256=GfkFvoMcKT2VpMWy3vrbyeKPMoR8xEo7UlZtLcVEon0,576
-bella_companion-0.0.29.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-bella_companion-0.0.29.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
-bella_companion-0.0.29.dist-info/RECORD,,

bella_companion-0.0.29.dist-info/entry_points.txt

@@ -1,3 +0,0 @@
-[console_scripts]
-bella=bella_companion.cli:main
-