Correct file permissions of docker files

.github/workflows/ci.yml

@@ -47,9 +47,9 @@ jobs:
       matrix:
         os: [ubuntu-20.04, ubuntu-22.04, macos-12, macos-13]
         fortran: [10, 11]
-        # exclude: # gfortran-11, gfortran-12 not available for ubuntu-20.04
-        # - os: ubuntu-20.04
-        #   fortran: 11
+        exclude: # gfortran-11, gfortran-12 not available for ubuntu-20.04
+        - os: ubuntu-20.04
+          fortran: 12
       fail-fast: false
 
     # -------------------------------------------------------------
@@ -73,9 +73,9 @@ jobs:
       # and the AtChem2 dependencies: CVODE, openlibm, numdiff, FRUIT
 
       # gfortran on ubuntu
-      #- name: Install gfortran-11 (ubuntu-20.04)
-      #  if: matrix.os == 'ubuntu-20.04' && matrix.fortran == 11
-      #  run: sudo apt-get install gfortran-11
+      - name: Install gfortran-11 (ubuntu-20.04)
+        if: matrix.os == 'ubuntu-20.04' && matrix.fortran == 11
+        run: sudo apt-get install gfortran-11
 
       # gfortran on macos
       - name: Install gfortran-10 (macos-12)

docker/entrypoint.sh

@@ -1,4 +1,4 @@
-#!/usr/bin/bash
+#!/bin/sh
 # -----------------------------------------------------------------------------
 #
 # Copyright (c) 2009 - 2012 Chris Martin, Kasia Boronska, Jenny Young,
@@ -16,41 +16,41 @@
 # -----------------------------------------------------------------------------
 
 # -----------------------------------------------------------------------------
-# This script is run everytime the container is run. 
+# This script is run everytime the container is run.
 #
-# First it copies the /atchem/ directory that is created during the build to 
+# First it copies the /atchem/ directory that is created during the build to
 # the home directory of the user running the container. This is for
 # compatibility with singularity, where the user running the container is not
-# root, and therefore cannot modify the model files in place. 
+# root, and therefore cannot modify the model files in place.
 #
 # Next it moves the user configuration from /data_transfer/ and copies it into
 # the ~/atchem/ directory. This /data_transfer/ directory is created when the
 # the user mounts a volume when running the container (e.g `docker run -v...`)
 #
 # We then move to the ~/atchem directory and build the model using the mechanism
-# specified by the user as a runtime argument to `docker run`. 
+# specified by the user as a runtime argument to `docker run`.
 #
-# Then the model is run by executing the newly built atchem2 file. 
+# Then the model is run by executing the newly built atchem2 file.
 #
 # On completion the atchem model output directory is copied to the data_transfer
 # directory and as such onto the host filesystem
 # -----------------------------------------------------------------------------
 
-# make a copy to home to allow for compatibility with singularity 
-\command cp -rf /atchem/ ~/ 
+# Make a copy to home to allow for compatibility with singularity
+\command cp -rf /atchem/ ~/
 
 # Transfer in user config
 \command cp -rf /data_transfer/* ~/atchem/
 
-# move into atchem dir
+# Move into atchem dir
 cd ~/atchem/
 
-# build model using user specified mechanism
+# Build model using user specified mechanism
 ./build/build_atchem2.sh $1
 echo $1
 
-# run model
+# Run model
 ./atchem2
 
-# copy outputs to data_transfer / host filesystem
-\command cp -rf ~/atchem/model/output /data_transfer/model/
+# Copy outputs to data_transfer / host filesystem
+\command cp -rf ~/atchem/model/output /data_transfer/model/

docker/install.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/sh
 # -----------------------------------------------------------------------------
 #
 # Copyright (c) 2009 - 2012 Chris Martin, Kasia Boronska, Jenny Young,
@@ -16,34 +16,34 @@
 # -----------------------------------------------------------------------------
 
 # -----------------------------------------------------------------------------
-# This is the install script that is run when the container is built. It 
+# This is the install script that is run when the container is built. It
 # installs the necessary dependacies for installing AtChem2 (gcc-gfortran,
 # wget, cmake and python3.11).
 #
-# It then runs the install scripts provided with the model (install_cvode.sh 
+# It then runs the install scripts provided with the model (install_cvode.sh
 # and install_openlibm.sh) to install additional dependancies required to build
 # the model.
-# 
-# Next it produces the Makefile from the skeleton, and amends the dependancy 
+#
+# Next it produces the Makefile from the skeleton, and amends the dependancy
 # paths.
-# 
+#
 # Finally it does some housekeeping, updating the build_atchem2.sh to be able
-# to find the python installation, and makes the docker entrypoint script 
-# executable. 
+# to find the python installation, and makes the docker entrypoint script
+# executable.
 # -----------------------------------------------------------------------------
 
 # Install dependancies from package repository
 dnf install -y which gcc-gfortran wget cmake python3.11
 
-# make directories
+# Make directories
 mkdir /atchem-lib
 # mkdir /atchem
 
-# move to /atchem so the dependacy installation scripts work correctly.
+# Move to /atchem so the dependacy installation scripts work correctly.
 cd atchem
 
 # Install dependancies to /atchem-lib
-./tools/install/install_cvode.sh /atchem-lib/ 
+./tools/install/install_cvode.sh /atchem-lib/
 ./tools/install/install_openlibm.sh /atchem-lib/
 
 # Change atchem dependancy paths and create Makefile from skeleton
@@ -52,4 +52,4 @@ sed -i 's,openlibm-0.8.1,/atchem-lib/openlibm-0.8.1,g' ./Makefile
 
 # Fix python command to match installed version
 sed -i "s/python/python3/g" ./build/build_atchem2.sh
-chmod +x docker/entrypoint.sh
+chmod +x docker/entrypoint.sh