Commit 8423f467 authored by Chris Jewell's avatar Chris Jewell
Browse files

Minor bugfixes

parent 06eadf38
......@@ -2,6 +2,7 @@
import os
import yaml
import pandas as pd
import ruffus as rf
......@@ -59,8 +60,9 @@ def run_pipeline(global_config, results_directory, cli_options):
input=run_mcmc,
filter=rf.formatter(),
output=wd("thin_samples.pkl"),
extras=[global_config],
)
def thin_samples(input_file, output_file):
def thin_samples(input_file, output_file, config):
thin_posterior(input_file, output_file, config["ThinPosterior"])
# Rt related steps
......
......@@ -4,7 +4,7 @@
#$ -P chicas
#$ -q gpu
#$ -l ngpus=1
# -l ncpus=2
# -l ncpus=4
#$ -l h_vmem=32G
#$ -l h_rt=12:00:00
#$ -j y
......
......@@ -21,6 +21,7 @@ gemlib = {git = "http://fhm-chicas-code.lancs.ac.uk/GEM/gemlib.git"}
xarray = "^0.16.1"
seaborn = "^0.11.0"
ruffus = "^2.8.4"
tensorflow = "^2.4.0"
[tool.poetry.dev-dependencies]
ipython = "^7.18.1"
......
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