Updates checking out CIME branch and using git-fleximod for CESM subm…

…odules

.github/workflows/testing.yml

@@ -109,6 +109,7 @@ jobs:
           CIME_MODEL: "cesm"
           CIME_DRIVER: "nuopc"
           CIME_TEST_PLATFORM: ubuntu-latest
+          SKIP_MODEL_SETUP: "true"
         run: |
           export SRC_PATH="${GITHUB_WORKSPACE}"
 
@@ -119,8 +120,6 @@ jobs:
           # GitHub runner home is different than container
           cp -rf /root/.cime /github/home/
 
-          git status
-
           pytest -vvv --cov=CIME --machine docker --no-fortran-run CIME/tests/test_unit*
 
   # Run system tests
@@ -163,27 +162,17 @@ jobs:
           CIME_TEST_PLATFORM: ubuntu-latest
         run: |
           export SRC_PATH="${GITHUB_WORKSPACE}"
+          export CIME_REMOTE=https://github.com/${{ github.event.pull_request.head.repo.full_name || github.repository }}
+          export CIME_BRANCH=${GITHUB_HEAD_REF:-${GITHUB_REF##*/}}
 
           source /entrypoint.sh
 
           # GitHub runner home is different than container
           cp -rf /root/.cime /github/home/
 
-          if [[ "${CIME_MODEL}" == "e3sm" ]]; then
-            git remote set-url origin https://github.com/${{ github.event.pull_request.head.repo.full_name || github.repository }}
-            git remote set-branches origin "*"
-            git fetch origin
-            git checkout ${GITHUB_HEAD_REF:-${GITHUB_REF##*/}}
-
-            # sync correct submodules
-            git submodule update
-
-            source /opt/conda/etc/profile.d/conda.sh
-
-            conda activate base
-          fi
+          source /opt/conda/etc/profile.d/conda.sh
 
-          git status
+          conda activate base
 
           pytest -vvv --cov=CIME --machine docker --no-fortran-run --no-teardown CIME/tests/test_sys*
       - uses: mxschmitt/action-tmate@v3

docker/Dockerfile

@@ -90,15 +90,13 @@ RUN git clone -b ${CIME_BRANCH} ${CIME_REPO} /src/cime
 ENV USER=root
 ENV LOGNAME=root
 ENV ESMFMKFILE=/opt/conda/lib/esmf.mk
+ENV SRC_PATH=/src
 
-WORKDIR /src/cime
+WORKDIR /src
 
 COPY .cime /root/.cime
 COPY entrypoint.sh /entrypoint.sh
 
-# TODO: REMOVE trigger
-ENV TRIGGER=0
-
 ENTRYPOINT [ "/entrypoint.sh" ]
 
 FROM base as slurm

docker/entrypoint.sh

@@ -6,14 +6,23 @@ SRC_PATH="${SRC_PATH:-`pwd`}"
 GIT_FLAGS="${GIT_FLAGS:---filter=tree:0}"
 # Shallow submodule checkout
 GIT_SUBMODULE_FLAGS="${GIT_SUBMODULE_FLAGS:---recommend-shallow}"
+SKIP_MODEL_SETUP="${SKIP_MODEL_CHECKOUT:-false}"
+CIME_REMOTE="${CIME_REMOTE:-https://github.com/ESMCI/cime}"
+CIME_BRANCH="${CIME_BRANCH:-master}"
 
 echo "DEBUG = ${DEBUG}"
 echo "SRC_PATH = ${SRC_PATH}"
 echo "GIT_FLAGS = ${GIT_FLAGS}"
 echo "GIT_SUBMODULE_FLAGS = ${GIT_SUBMODULE_FLAGS}"
+echo "SKIP_MODEL_SETUP = ${SKIP_MODEL_SETUP}"
+echo "CIME_REMOTE = ${CIME_REMOTE}"
+echo "CIME_BRANCH = ${CIME_BRANCH}"
 
-if [[ "$(echo ${DEBUG} | tr -s '[:upper:]' '[:lower:]')" == "true" ]]
-then
+function to_lowercase() {
+    echo "${!1}" | tr -s '[:upper:]' '[:lower:]' 
+}
+
+if [[ "$(to_lowercase DEBUG)" == "true" ]]; then
     set -x
 fi
 
@@ -22,7 +31,7 @@ fi
 #
 # TODO need to make an offical PR this is temporary.
 #######################################
-function fix_mct_arflags {
+function fix_mct_arflags() {
     local mct_path="${1}"
 
     # TODO make PR to fix
@@ -48,64 +57,62 @@ function fix_gitmodules() {
     sed -i".bak" "s/git@github.com:/https:\/\/github.com\//g" "${1}/.gitmodules"
 }
 
-if [[ "${CIME_MODEL}" == "e3sm" ]]
-then
-    echo "Setting up E3SM"
-
-    [[ ! -e "${SRC_PATH}/E3SM" ]] && git clone -b ${E3SM_BRANCH:-master} ${GIT_FLAGS} ${E3SM_REPO:-https://github.com/E3SM-Project/E3SM} "${SRC_PATH}/E3SM"
-
-    pushd "${SRC_PATH}/E3SM"
+if [[ "${SKIP_MODEL_SETUP}" == "false" ]]; then
+    if [[ "${CIME_MODEL}" == "e3sm" ]]; then
+        echo "Setting up E3SM"
 
-    git config --global --add safe.directory "*"
+        [[ ! -e "${SRC_PATH}/E3SM" ]] && git clone -b ${E3SM_BRANCH:-master} ${GIT_FLAGS} ${E3SM_REPO:-https://github.com/E3SM-Project/E3SM} "${SRC_PATH}/E3SM"
 
-    # fix E3SM gitmodules
-    fix_gitmodules "${PWD}"
+        pushd "${SRC_PATH}/E3SM"
 
-    git status
+        git config --global --add safe.directory "*"
 
-    # checkout submodules
-    git submodule update --init "${GIT_SUBMODULE_FLAGS}"
+        # fix E3SM gitmodules
+        fix_gitmodules "${PWD}"
 
-    # fix mct arflags flags
-    fix_mct_arflags "${SRC_PATH}/E3SM/externals/mct"
+        git status
 
-    pushd cime
+        # checkout submodules
+        git submodule update --init "${GIT_SUBMODULE_FLAGS}"
 
-    # fix CIME gitmodules
-    fix_gitmodules "${PWD}"
+        # fix mct arflags flags
+        fix_mct_arflags "${SRC_PATH}/E3SM/externals/mct"
 
-    # checkout submodules
-    git submodule update --init "${GIT_SUBMODULE_FLAGS}"
+        pushd cime
+    elif [[ "${CIME_MODEL}" == "cesm" ]]; then
+        echo "Setting up CESM"
 
-    # link v2 config_machines
-    ln -sf /root/.cime/config_machines.v2.xml /root/.cime/config_machines.xml
-elif [[ "${CIME_MODEL}" == "cesm" ]]
-then
-    echo "Setting up CESM"
-
-    [[ ! -e "${SRC_PATH}/CESM" ]] && git clone -b ${CESM_BRANCH:-master} ${GIT_FLAGS} ${E3SM_REPO:-https://github.com/ESCOMP/CESM} "${SRC_PATH}/CESM"
+        [[ ! -e "${SRC_PATH}/CESM" ]] && git clone -b ${CESM_BRANCH:-master} ${GIT_FLAGS} ${E3SM_REPO:-https://github.com/ESCOMP/CESM} "${SRC_PATH}/CESM"
 
-    pushd "${SRC_PATH}/CESM"
+        pushd "${SRC_PATH}/CESM"
 
-    git config --global --add safe.directory "*"
+        git config --global --add safe.directory "*"
 
-    # fix CIME gitmodules
-    fix_gitmodules "${PWD}"
+        ./bin/git-fleximod update
 
-    git status
+        git status
 
-    git submodule update --init "${GIT_SUBMODULE_FLAGS}"
-    git submodule update --init "${GIT_SUBMODULE_FLAGS}" --recursive components/cdeps
+        pushd cime
+    fi
+fi
 
-    pushd cime
+# Expect current directory to be CIME
+git remote set-url origin "${CIME_REMOTE}"
+git remote set-branches origin "*"
+git fetch origin
+git checkout "${CIME_BRANCH}"
 
-    fix_gitmodules "${PWD}"
+# Sync submodules
+git submodule update --init
 
-    # update CIME submodules
-    git submodule update --init "${GIT_SUBMODULE_FLAGS}"
+git status
 
+if [[ "${CIME_MODEL}" == "e3sm" ]]; then
+    # link v2 config_machines
+    ln -sf ~/.cime/config_machines.v2.xml ~/.cime/config_machines.xml
+elif [[ "${CIME_MODEL}" == "cesm" ]]; then
     # link v3 config_machines
-    ln -sf /root/.cime/config_machines.v3.xml /root/.cime/config_machines.xml
+    ln -sf ~/.cime/config_machines.v3.xml ~/.cime/config_machines.xml
 fi
 
 # load batch specific entrypoint