From 7ab1743d0d1675e8e02c1bbff5c040ac0cc601bb Mon Sep 17 00:00:00 2001
From: Daniele Rapetti <5535617+Iximiel@users.noreply.github.com>
Date: Thu, 30 Nov 2023 13:37:13 +0100
Subject: [PATCH 1/5] testing the CI

---
 .github/workflows/linuxWF.yml | 86 +++++++++++++++++++++++++++++++++++
 1 file changed, 86 insertions(+)

diff --git a/.github/workflows/linuxWF.yml b/.github/workflows/linuxWF.yml
index 0811812765..c3ab78ca08 100644
--- a/.github/workflows/linuxWF.yml
+++ b/.github/workflows/linuxWF.yml
@@ -38,6 +38,7 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: 3.9
+        cache: pip #this will save some time in getting the requirements
     - name: Set paths
       run: |
         echo "$HOME/opt/bin" >> $GITHUB_PATH
@@ -181,3 +182,88 @@ jobs:
         GIT_TOKEN: ${{ secrets.GIT_TOKEN_PLUMEDBOT }}
       run: |
          .ci/push doc
+    - name: Saving "$HOME/opt"
+      if:  matrix.variant == '-mpi-' 
+      uses: actions/cache/save@v3
+      with:
+        path: $HOME/opt
+        key: ccache-plumedInstall-linux${{ matrix.variant }}hash-${{ github.sha }}
+              
+    
+  linux-pycv:
+    needs: linux
+    runs-on: ubuntu-22.04
+    strategy:
+      fail-fast: false
+      matrix:
+        variant:
+        - -mpi-
+# temporarily commented out
+# see https://github.com/plumed/plumed2/issues/976
+#        - -intel-
+    steps:
+    - uses: actions/checkout@v3
+    - name: Restoring "$HOME/opt"
+      if:  matrix.variant == '-mpi-' 
+      uses: actions/cache/restore@v3
+      with:
+        path: $HOME/opt
+        key: ccache-plumedInstall-linux${{ matrix.variant }}hash-${{ github.sha }}
+    - uses: actions/cache@v3
+      with:
+        path: ~/.ccache
+        key: ccache-reset1-linux${{ matrix.variant }}hash-${{ github.sha }}
+        restore-keys: ccache-reset1-linux${{ matrix.variant }}hash-
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+        cache: pip #this will save some time in getting the requirements
+    - name: Set paths
+      run: |
+        echo "$HOME/opt/bin" >> $GITHUB_PATH
+        # path required for pytest:
+        echo "$HOME/.local/bin" >> $GITHUB_PATH
+        echo "CPATH=$HOME/opt/include:$CPATH" >> $GITHUB_ENV
+        echo "INCLUDE=$HOME/opt/include:$INCLUDE" >> $GITHUB_ENV
+        echo "LIBRARY_PATH=$HOME/opt/lib:$LIBRARY_PATH" >> $GITHUB_ENV
+        echo "LD_LIBRARY_PATH=$HOME/opt/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+        echo "PYTHONPATH=$HOME/opt/lib/plumed/python:$PYTHONPATH" >> $GITHUB_ENV
+    - name: Install generic packages
+      run: |
+        sudo apt-get update -qq
+        sudo apt-get install -y libatlas-base-dev
+        sudo apt-get install -y libfftw3-dev
+        sudo apt-get install -y gsl-bin
+        sudo apt-get install -y libgsl0-dev
+        sudo apt-get install -y ccache
+        sudo apt-get install -y libboost-serialization-dev
+        sudo apt-get install -y libopenmpi-dev openmpi-bin
+        echo "CC=mpicc" >> $GITHUB_ENV
+        echo "CXX=mpic++" >> $GITHUB_ENV
+        echo "OMPI_MCA_btl_base_warn_component_unused=0" >> $GITHUB_ENV
+        echo "OMPI_MCA_btl_base_verbose=0" >> $GITHUB_ENV
+        echo "OMPI_MCA_plm=isolated" >> $GITHUB_ENV
+        echo "OMPI_MCA_btl_vader_single_copy_mechanism=none" >> $GITHUB_ENV
+        echo "OMPI_MCA_rmaps_base_oversubscribe=yes" >> $GITHUB_ENV
+    - name: Install python packages
+      run: |
+        python -m pip install --upgrade pip
+        pip install --user Cython
+        pip install --user numpy
+        pip install --user pytest
+        pip install --user pybind11
+        pip install --user six ;
+        pip install --user pandas ;
+        pip install --user mdtraj ;
+        pip install --user MDAnalysis ;
+        python -c "import MDAnalysis" ;
+        python -c "import mdtraj" ;
+        pip install --user mpi4py
+        python -c "import mpi4py"
+    - name: compile and test pycv
+      working-directory: ./plugins/pycv/
+      run: |
+          ./prepareMakeForDevelop.sh  
+          make check
+    
\ No newline at end of file

From 000f00c7908eb50c48d6299099eee8c488b8f009 Mon Sep 17 00:00:00 2001
From: Daniele Rapetti <5535617+Iximiel@users.noreply.github.com>
Date: Thu, 30 Nov 2023 15:23:01 +0100
Subject: [PATCH 2/5] test II on the workflow

---
 .github/workflows/ci.yml      | 24 ++++++++++++------------
 .github/workflows/linuxWF.yml | 31 ++++++++++++++++++++++++++-----
 2 files changed, 38 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2fcdd99f45..b9a307f53f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -19,18 +19,18 @@ jobs:
     uses: ./.github/workflows/linuxWF.yml
     secrets: inherit
 
-  codecheck:
-    uses: ./.github/workflows/codecheckWF.yml
-    secrets: inherit
+  # codecheck:
+  #   uses: ./.github/workflows/codecheckWF.yml
+  #   secrets: inherit
 
-  mac:
-    uses: ./.github/workflows/macWF.yml
-    secrets: inherit
+  # mac:
+  #   uses: ./.github/workflows/macWF.yml
+  #   secrets: inherit
         
-  docker:
-    uses: ./.github/workflows/dockerWF.yml
-    secrets: inherit
+  # docker:
+  #   uses: ./.github/workflows/dockerWF.yml
+  #   secrets: inherit
 
-  conda:
-    uses: ./.github/workflows/condaWF.yml
-    secrets: inherit
+  # conda:
+  #   uses: ./.github/workflows/condaWF.yml
+  #   secrets: inherit
diff --git a/.github/workflows/linuxWF.yml b/.github/workflows/linuxWF.yml
index c3ab78ca08..add56768d0 100644
--- a/.github/workflows/linuxWF.yml
+++ b/.github/workflows/linuxWF.yml
@@ -13,17 +13,38 @@ env:
   CXX: g++
 
 jobs:
+  linuxCachingPip:
+    runs-on: ubuntu-22.04
+    steps:
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+        cache: pip #this will save some time in getting the requirements
+    - name: Install python packages needed for tests
+      run: |
+          python -m pip install --upgrade pip
+          pip install --user Cython
+          pip install --user numpy
+          pip install --user pytest
+          pip install --user six ;
+          pip install --user pandas ;
+          pip install --user mdtraj ;
+          pip install --user MDAnalysis ;
+    
   linux:
+    needs: linuxCachingPip
     runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:
         variant:
-        - -doc-mpi-
+        #commenting the ci for testing
+        #- -doc-mpi-
         - -mpi-
-        - -coverage-mpi-
-        - -debug-
-        - -debug-mpi-
+        #- -coverage-mpi-
+        #- -debug-
+        #- -debug-mpi-
 # temporarily commented out
 # see https://github.com/plumed/plumed2/issues/976
 #        - -intel-
@@ -186,7 +207,7 @@ jobs:
       if:  matrix.variant == '-mpi-' 
       uses: actions/cache/save@v3
       with:
-        path: $HOME/opt
+        path: ~/opt
         key: ccache-plumedInstall-linux${{ matrix.variant }}hash-${{ github.sha }}
               
     

From 6991d565562120bd027ebdfdd93c85c148522174 Mon Sep 17 00:00:00 2001
From: Daniele Rapetti <5535617+Iximiel@users.noreply.github.com>
Date: Thu, 30 Nov 2023 15:30:13 +0100
Subject: [PATCH 3/5] test III on the workflow

---
 .github/workflows/linuxWF.yml | 2 ++
 python/requirements.txt       | 8 ++++++++
 2 files changed, 10 insertions(+)
 create mode 100644 python/requirements.txt

diff --git a/.github/workflows/linuxWF.yml b/.github/workflows/linuxWF.yml
index add56768d0..12309918bd 100644
--- a/.github/workflows/linuxWF.yml
+++ b/.github/workflows/linuxWF.yml
@@ -16,11 +16,13 @@ jobs:
   linuxCachingPip:
     runs-on: ubuntu-22.04
     steps:
+    - uses: actions/checkout@v3
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
         python-version: 3.9
         cache: pip #this will save some time in getting the requirements
+        cache-dependency-path: ./python/requirements
     - name: Install python packages needed for tests
       run: |
           python -m pip install --upgrade pip
diff --git a/python/requirements.txt b/python/requirements.txt
new file mode 100644
index 0000000000..e9366fdbac
--- /dev/null
+++ b/python/requirements.txt
@@ -0,0 +1,8 @@
+#requirements for the tests in the CI
+Cython
+numpy
+pytest
+six
+pandas
+mdtraj
+MDAnalysis

From 5e3e8a69c670311a260506aa126818ffe9bf1c75 Mon Sep 17 00:00:00 2001
From: Daniele Rapetti <5535617+Iximiel@users.noreply.github.com>
Date: Thu, 30 Nov 2023 15:32:56 +0100
Subject: [PATCH 4/5] test III(2) on the workflow

---
 .github/workflows/linuxWF.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/linuxWF.yml b/.github/workflows/linuxWF.yml
index 12309918bd..45d4854b49 100644
--- a/.github/workflows/linuxWF.yml
+++ b/.github/workflows/linuxWF.yml
@@ -22,7 +22,7 @@ jobs:
       with:
         python-version: 3.9
         cache: pip #this will save some time in getting the requirements
-        cache-dependency-path: ./python/requirements
+        cache-dependency-path: ./python/requirements.txt
     - name: Install python packages needed for tests
       run: |
           python -m pip install --upgrade pip
@@ -62,6 +62,7 @@ jobs:
       with:
         python-version: 3.9
         cache: pip #this will save some time in getting the requirements
+        cache-dependency-path: ./python/requirements.txt
     - name: Set paths
       run: |
         echo "$HOME/opt/bin" >> $GITHUB_PATH
@@ -242,6 +243,7 @@ jobs:
       with:
         python-version: 3.9
         cache: pip #this will save some time in getting the requirements
+        cache-dependency-path: ./python/requirements.txt
     - name: Set paths
       run: |
         echo "$HOME/opt/bin" >> $GITHUB_PATH

From 38451318cc55cab4204c2baf2cb8fad7e91fc3be Mon Sep 17 00:00:00 2001
From: Daniele Rapetti <5535617+Iximiel@users.noreply.github.com>
Date: Thu, 30 Nov 2023 16:30:07 +0100
Subject: [PATCH 5/5] test III(3) on the workflow

---
 .github/workflows/ci.yml      | 2 +-
 .github/workflows/linuxWF.yml | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b9a307f53f..637a4f131a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,7 +1,7 @@
 name: CI
 
 on:
-  push:
+  #push:
   pull_request:
 
 env:
diff --git a/.github/workflows/linuxWF.yml b/.github/workflows/linuxWF.yml
index 45d4854b49..cb77d48731 100644
--- a/.github/workflows/linuxWF.yml
+++ b/.github/workflows/linuxWF.yml
@@ -228,10 +228,9 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - name: Restoring "$HOME/opt"
-      if:  matrix.variant == '-mpi-' 
       uses: actions/cache/restore@v3
       with:
-        path: $HOME/opt
+        path: ~/opt
         key: ccache-plumedInstall-linux${{ matrix.variant }}hash-${{ github.sha }}
     - uses: actions/cache@v3
       with: