Wed 16 Mar 2022 12:29:44 PM EDT
python3 and packages required can be installed system wide or a conda env
I suggest using conda:
Install miniconda or anaconda normally if not already installed
conda create -n outbreak-reporter
conda activate outbreak-reporter
conda install pandas numpy matplotlib openpyxl scipy pytables
conda install -c conda-forge openjdk parallel
Conda package for texlive is currently not working quite right, so need to install systemwide
sudo apt install texlive-full
Other latex installtions will probably work fine if they provide pdflatex
conda activate outbreak-reporter
cp -r skel <short_name>
cd <short_name>
mkdir official
copy any SITSTAT or lifecyle docs to official directory
edit main.cfg
../bin/fetch_and_process_temperatures.py
../bin/setup_medfoes.py
cd medfoes
./run_mfp_local.sh
wait for medfoes runs to complete
cd ..
../bin/make_report.py
report.pdf is the final output
To update...
start from:
../bin/fetch_and_process_temperatures.py
if only current year needs update, can run
./run_mfp_current.sh instead of ./run_mfp_local.sh from the medfoes directory
To run on a cluster using SGE,
run ../../bin/do_mfp_runs_SGE.sh instead of ./run_mfp_local.sh from the medfoes directory
# packages in environment at <snip>/miniconda3/envs/outbreak-reporter:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
alsa-lib 1.2.3 h516909a_0 conda-forge
blosc 1.21.0 h9c3ff4c_0 conda-forge
brotli 1.0.9 h7f98852_6 conda-forge
brotli-bin 1.0.9 h7f98852_6 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2021.10.8 ha878542_0 conda-forge
certifi 2021.10.8 py310hff52083_1 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
et_xmlfile 1.0.1 py_1001 conda-forge
expat 2.4.7 h27087fc_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.13.96 h8e229c2_2 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.30.0 py310h5764c6d_0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
gst-plugins-base 1.18.5 hf529b03_3 conda-forge
gstreamer 1.18.5 h9f60fe5_3 conda-forge
hdf5 1.12.1 nompi_h2386368_104 conda-forge
icu 69.1 h9c3ff4c_0 conda-forge
jbig 2.1 h7f98852_2003 conda-forge
jpeg 9e h7f98852_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.0 py310hbf28c38_0 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 13_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h7f98852_6 conda-forge
libbrotlidec 1.0.9 h7f98852_6 conda-forge
libbrotlienc 1.0.9 h7f98852_6 conda-forge
libcblas 3.9.0 13_linux64_openblas conda-forge
libclang 13.0.1 default_hc23dcda_0 conda-forge
libcurl 7.82.0 h7bff187_0 conda-forge
libdeflate 1.10 h7f98852_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.10 h9b69904_4 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 11.2.0 h1d223b6_14 conda-forge
libgfortran-ng 11.2.0 h69a702a_14 conda-forge
libgfortran5 11.2.0 h5c6108e_14 conda-forge
libglib 2.70.2 h174f98d_4 conda-forge
libgomp 11.2.0 h1d223b6_14 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 13_linux64_openblas conda-forge
libllvm13 13.0.1 hf817b99_2 conda-forge
libnghttp2 1.47.0 h727a467_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.18 pthreads_h8fe5266_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libpq 14.2 hd57d9b9_0 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_14 conda-forge
libtiff 4.3.0 h542a066_3 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp 1.2.2 h3452ae3_0 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxkbcommon 1.0.3 he3ba5ed_0 conda-forge
libxml2 2.9.12 h885dcf4_1 conda-forge
libzlib 1.2.11 h36c2ea0_1013 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
lzo 2.10 h516909a_1000 conda-forge
matplotlib 3.5.1 py310hff52083_0 conda-forge
matplotlib-base 3.5.1 py310h23f4a51_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.0.28 ha770c72_0 conda-forge
mysql-libs 8.0.28 hfa10184_0 conda-forge
ncurses 6.3 h9c3ff4c_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
nspr 4.32 h9c3ff4c_1 conda-forge
nss 3.74 hb5efdd6_0 conda-forge
numexpr 2.8.0 py310hcff4476_101 conda-forge
numpy 1.22.3 py310h45f3432_0 conda-forge
openjdk 8.0.312 h7f98852_0 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openpyxl 3.0.9 pyhd8ed1ab_0 conda-forge
openssl 1.1.1l h7f98852_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandas 1.4.1 py310hb5077e9_0 conda-forge
parallel 20220222 ha770c72_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
perl 5.32.1 2_h7f98852_perl5 conda-forge
pillow 9.0.1 py310he619898_2 conda-forge
pip 22.0.4 pyhd8ed1ab_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pyparsing 3.0.7 pyhd8ed1ab_0 conda-forge
pyqt 5.12.3 py310hff52083_8 conda-forge
pyqt-impl 5.12.3 py310h1f8e252_8 conda-forge
pyqt5-sip 4.19.18 py310h122e73d_8 conda-forge
pyqtchart 5.12 py310hfcd6d55_8 conda-forge
pyqtwebengine 5.12.1 py310hfcd6d55_8 conda-forge
pytables 3.7.0 py310hf5df6ce_0 conda-forge
python 3.10.2 h85951f9_4_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.10 2_cp310 conda-forge
pytz 2021.3 pyhd8ed1ab_0 conda-forge
qt 5.12.9 ha98a1a1_5 conda-forge
readline 8.1 h46c0cb4_0 conda-forge
scipy 1.8.0 py310hea5193d_1 conda-forge
setuptools 60.9.3 py310hff52083_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlite 3.37.0 h9cd32fc_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tornado 6.1 py310h6acc77f_2 conda-forge
tzdata 2021e he74cb21_0 conda-forge
unicodedata2 14.0.0 py310h6acc77f_0 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zlib 1.2.11 h36c2ea0_1013 conda-forge
zstd 1.5.2 ha95c52a_0 conda-forge