v0.2

Author: ppernot

R/massCalc.R

@@ -1,7 +1,7 @@
 filterFormula <- function (sp) {
   # Normalize chemical formula for mass estimation
   if(is.null(stoechFilters))
-    stop(">>> Need stoechFilters !")
+    stop(">>> Need stoechFilters in global Env. !")
   sp1 = sp
   for(i in 1:nrow(stoechFilters))
     sp1 = sub(stoechFilters[i,1], stoechFilters[i,2], sp1)

README.md

@@ -6,21 +6,23 @@ UI to manage [MC-ChemDB](https://github.com/ppernot/MC-ChemDB).
 
 ## News
 
-* `2022/07/21` First docker version to handle neutral reactions with three main functions:
+* `2022/07/21` First docker version (v0.1) to handle neutral reactions with three main functions:
 
     1. Open and edit DB files; create new DB version
 
     2. Parse the DB files to check the consistency (names, masses, mass balance...)
 
     3. Generate MC samples and plot resulting reaction rates as a function of temperature
     and density.
+
+* `2022/07/29` v0.2
+
+    1. Add ion/molecule reactions (edit/parse, sample). No `Save` feature yet...
 
 ## To Be Done...
 
 * Add possibility to Import/Export MC-ChemDB (to and from github ?)
 
-* Manage ion-molecule reactions
-
 * Manage photo-processes
 
 

compressDB.sh

@@ -1,3 +1,5 @@
-tar -cvzf ChemDB.tar.gz \
+tar --atime-preserve -cvzf ChemDB.tar.gz \
   ../MC-ChemDB/Neutrals/Source/v_1.* \
-  ../MC-ChemDB/Ions/Source/v_1.3/Data/*/data.csv
+  ../MC-ChemDB/Ions/Source/v_1.3/Data/*/data.csv \
+  ../MC-ChemDB/Ions/Tmp/v_1.3/Reactions \
+  ../MC-ChemDB/Doc

docker/Dockerfile

@@ -2,16 +2,18 @@ FROM ppernot1/shiny_base
 
 RUN apt-get install -y --no-install-recommends libharfbuzz-dev libfribidi-dev
 
-## renv
+# renv
 ENV RENV_VERSION 0.15.5
 RUN Rscript -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
 RUN Rscript -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"
 
 RUN mkdir MC-ChemDBUI
-COPY .Rprofile /MC-ChemDBUI/
-COPY renv/activate.R /MC-ChemDBUI/renv/activate.R
-COPY renv.lock /MC-ChemDBUI/renv.lock
 WORKDIR /MC-ChemDBUI
+COPY .Rprofile .
+#ADD renv.tar.gz . # Pb unresolved shared libs...
+COPY renv/activate.R ./renv/activate.R
+COPY renv.lock ./renv.lock
+#WORKDIR /MC-ChemDBUI
 RUN R -e 'renv::consent(TRUE)' \
  && R -e 'renv::restore()'
 
@@ -20,16 +22,24 @@ WORKDIR /
 RUN mkdir ChemDBPublic
 ADD ChemDB.tar.gz /
 
-## app files
-COPY global.R /MC-ChemDBUI/
-COPY ui.R /MC-ChemDBUI/
-COPY server.R /MC-ChemDBUI/
-COPY ui_files /MC-ChemDBUI/ui_files/
-COPY server_files /MC-ChemDBUI/server_files/
-COPY R /MC-ChemDBUI/R/
-COPY data /MC-ChemDBUI/data/
+
+## Sampler files
 WORKDIR /MC-ChemDBUI
+COPY Sampler ./Sampler/
+WORKDIR /MC-ChemDBUI/Sampler/Ranlib/src
+RUN ./comp
+WORKDIR /MC-ChemDBUI/Sampler
+RUN ./compile
 
+## app files
+WORKDIR /MC-ChemDBUI
+COPY global.R .
+COPY ui.R .
+COPY server.R .
+COPY ui_files ./ui_files/
+COPY server_files ./server_files/
+COPY R ./R/
+COPY data ./data/
 
 ## change user from root ### BREAKS renv links !!!
 #RUN addgroup --system app \

docker/commands.txt

@@ -1,6 +1,7 @@
 BUILD :
     1/ cd MC-ChemDBUI
-    2/ docker build -t ppernot1/mc-chemdbui:v0.1 -t ppernot1/mc-chemdbui:latest -f docker/Dockerfile .
+    1.a/ source compressDB.sh
+    2/ docker build -t ppernot1/mc-chemdbui:v0.2 -t ppernot1/mc-chemdbui:latest -f docker/Dockerfile .
     3/ docker login
     4/ docker image push --all-tags ppernot1/mc-chemdbui
 

global.R

@@ -1,4 +1,4 @@
-version = 0.0
+version = 0.2
 
 # Options ####
 Sys.setlocale(category = "LC_NUMERIC", locale = "C")

renv/.gitignore

@@ -0,0 +1,6 @@
+library/
+local/
+cellar/
+lock/
+python/
+staging/