Merge pull request #5 from pnnl-predictive-phenomics/4-reconfiguring-…

…memote

4 reconfiguring memote

.github/workflows/diff-pr.yml

@@ -3,12 +3,15 @@ name: memote-diff
 on:
   pull_request:
     branches:
-      - master
+      - main
 
 jobs:
   diff:
     runs-on: ubuntu-latest
-
+    permissions:
+      contents: write
+      issues: write
+      pull-requests: write
     steps:
     - uses: actions/checkout@v2
       with:
@@ -24,7 +27,7 @@ jobs:
       run: |
         model=$(awk -F '=' '{if (! ($0 ~ /^;/) && $0 ~ /model/) print $2}' memote.ini | tr -d ' ')
         deployment=$(awk -F '=' '{if (! ($0 ~ /^;/) && $0 ~ /deployment/) print $2}' memote.ini | tr -d ' ')
-        git show "origin/master:${model}" > "prev_${model}"
+        git show "origin/main:${model}" > "prev_${model}"
         memote report diff --filename "diff${GITHUB_SHA}.html" "$model" "prev_${model}"
         git checkout $deployment
         git pull

.github/workflows/memote.yml

@@ -3,7 +3,7 @@ name: memote
 on:
   push:
     branches:
-    - master
+    - main
 
 jobs:
   report:

csc052/data/experiments.yml

@@ -1,7 +1,20 @@
 version: "0.1"
 medium:
   path: "media/"
+  definitions:
+    whole_medium_no_carbon:
+      filename: "csc052C-less_media.csv"
+      label: "All medium metabolites except the ones with Carbon"
+    min_media_no_carbon:
+      filename: "min_medium_csc052C-less_media.csv"
+      label: "Minimal media with no carbon"
 essentiality:
   path: "essentiality/"
 growth:
   path: "growth/"
+  experiments:
+    biolog_carbon:
+      medium: min_media_no_carbon
+      filename: "biolog_carbon_toyonensis.csv"
+      label: "no_carbon data"
+minimal_growth_rate: 0.05

csc052/data/growth/biolog_carbon_toyonensis.csv

@@ -0,0 +1,60 @@
+exchange,growth,uptake
+EX_cs_c_e,True,10
+EX_dextrin_e,True,10
+EX_glycogen_e,True,10
+EX_mannan_e,False,10
+EX_pectin_e,True,10
+EX_acgal_e,False,10
+EX_acnam_e,False,10
+EX_arab__D_e,False,10
+EX_abt__D_e,False,10
+EX_abt__L_e,False,10
+EX_arbt_e,True,10
+EX_drib_e,False,10
+EX_madg_e,True,10
+EX_pala_e,True,10
+EX_raffin_e,False,10
+EX_salcn_e,True,10
+EX_srb__L_e,False,10
+EX_stys_e,True,10
+EX_tag__D_e,True,10
+EX_xylt_e,False,10
+EX_but_e,True,10
+EX_dca_e,False,10
+EX_hxa_e,False,10
+EX_citac_e,True,10
+EX_citm_e,True,10
+EX_gam_e,True,10
+EX_salc_e,False,10
+EX_4hbz_e,False,10
+EX_glyclt_e,True,10
+EX_itacon_e,False,10
+EX_5dglcn_e,True,10
+EX_malon_e,True,10
+EX_oxa_e,True,10
+EX_quin_e,True,10
+EX_Dara14lac_e,True,10
+EX_sebacid_e,False,10
+EX_tartr__D_e,True,10
+EX_tartr__L_e,True,10
+EX_ad_e,False,10
+EX_acglu_e,True,10
+EX_arg__L_e,True,10
+EX_gly_e,True,10
+EX_his__L_e,True,10
+EX_hom__L_e,False,10
+EX_4hpro_DC_e,True,10
+EX_ile__L_e,True,10
+EX_leu__L_e,True,10
+EX_lys__L_e,True,10
+EX_met__L_e,True,10
+EX_orn__L_e,True,10
+EX_phe__L_e,True,10
+EX_5oxpro_e,True,10
+EX_val__L_e,True,10
+EX_crn_e,True,10
+EX_ptrc_e,True,10
+EX_dha_e,True,10
+EX_btd_RR_e,True,10
+EX_diact_e,False,10
+EX_R_actn_e,True,10

csc052/data/media/csc052C-less_media.csv

@@ -0,0 +1,28 @@
+exchange,uptake
+EX_2m35mdntha_e,1000
+EX_aso3_e,1000
+EX_aso4_e,1000
+EX_fe2_e,1000
+EX_fe3_e,1000
+EX_h2o2_e,1000
+EX_h2o_e,1000
+EX_h2s_e,1000
+EX_h_e,1000
+EX_ham_e,1000
+EX_k_e,1000
+EX_mg2_e,1000
+EX_mn2_e,1000
+EX_mobd_e,1000
+EX_nh4_e,1000
+EX_no2_e,1000
+EX_no3_e,1000
+EX_o2_e,1000
+EX_pi_e,1000
+EX_ppi_e,1000
+EX_s_e,1000
+EX_so3_e,1000
+EX_so4_e,1000
+EX_tet_e,1000
+EX_tnt_e,1000
+EX_tsul_e,1000
+EX_zn2_e,1000

csc052/data/media/min_medium_csc052C-less_media.csv

@@ -0,0 +1,12 @@
+exchange,uptake
+EX_fe2_e,1000
+EX_fe3_e,1000
+EX_h2o2_e,1000
+EX_h2o_e,1000
+EX_k_e,1000
+EX_mg2_e,1000
+EX_mn2_e,1000
+EX_o2_e,1000
+EX_s_e,1000
+EX_so4_e,1000
+EX_zn2_e,1000

csc052/scripts/ghactions_deploy.sh

@@ -10,7 +10,7 @@ location=$(awk -F '=' '{if (! ($0 ~ /^;/) && $0 ~ /location/) print $2}' memote.
 git config --global user.email "${GITHUB_ACTOR}@users.noreply.github.com"
 git config --global user.name "${GITHUB_ACTOR}"
 
-if [[ "${GITHUB_EVENT_NAME}" == "pull_request" || "${GITHUB_REPOSITORY}" != "pnnl-predictive-phenomics/csc009" ]]; then
+if [[ "${GITHUB_EVENT_NAME}" == "pull_request" || "${GITHUB_REPOSITORY}" != "pnnl-predictive-phenomics/csc052" ]]; then
     echo "Untracked build."
     memote run --ignore-git
 		echo "Skip deploy."