From 0cfa4fcf343ad69122ad5081633b0ed40e06757b Mon Sep 17 00:00:00 2001
From: dkazanc <dkazanc@hotmail.com>
Date: Mon, 12 Aug 2024 16:55:00 +0100
Subject: [PATCH 1/6] adding actions ci for the library build

---
 .../workflows/libtomophantom_conda_upload.yml | 42 +++++++++++++++++++
 .../workflows/tomophantom_conda_upload.yml    | 10 ++---
 .scripts/conda_upload.sh                      |  2 +-
 .scripts/conda_upload_lib.sh                  | 20 +++++++++
 4 files changed, 68 insertions(+), 6 deletions(-)
 create mode 100644 .github/workflows/libtomophantom_conda_upload.yml
 create mode 100755 .scripts/conda_upload_lib.sh

diff --git a/.github/workflows/libtomophantom_conda_upload.yml b/.github/workflows/libtomophantom_conda_upload.yml
new file mode 100644
index 0000000..603433b
--- /dev/null
+++ b/.github/workflows/libtomophantom_conda_upload.yml
@@ -0,0 +1,42 @@
+name: libtomophantom_conda_upload
+
+on: [push]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-20.04
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout repository code
+        uses: actions/checkout@v4
+        with:
+          ref: "master"
+          fetch-depth: 0
+
+      # setup Python 3.11
+      - name: Setup Python 3.11
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies with Conda
+        run: |
+          $CONDA/bin/conda install -c conda-forge conda-build anaconda-client
+          $CONDA/bin/conda install -c conda-forge cmake
+          $CONDA/bin/conda update conda
+          $CONDA/bin/conda update conda-build
+          $CONDA/bin/conda list
+
+      - name: Decrypt a secret
+        run: ./.scripts/decrypt_secret.sh
+        env:
+          LARGE_SECRET_PASSPHRASE: ${{ secrets.LARGE_SECRET_PASSPHRASE }}
+
+      - name: Upload the tested package to conda cloud
+        run: |
+          chmod +x ./.scripts/conda_upload_lib.sh
+          ./.scripts/conda_upload_lib.sh
diff --git a/.github/workflows/tomophantom_conda_upload.yml b/.github/workflows/tomophantom_conda_upload.yml
index 6091c43..f857971 100644
--- a/.github/workflows/tomophantom_conda_upload.yml
+++ b/.github/workflows/tomophantom_conda_upload.yml
@@ -1,4 +1,4 @@
-name: tomohantom_conda_upload
+name: tomophantom_conda_upload
 
 on: [push]
 
@@ -12,16 +12,16 @@ jobs:
 
     steps:
       - name: Checkout repository code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: "master"
           fetch-depth: 0
 
-      # setup Python 3.9
-      - name: Setup Python 3.9
+      # setup Python 3.11
+      - name: Setup Python 3.11
         uses: actions/setup-python@v2
         with:
-          python-version: 3.9
+          python-version: 3.11
 
       - name: Install dependencies with Conda
         run: |
diff --git a/.scripts/conda_upload.sh b/.scripts/conda_upload.sh
index 0b1ecfa..f91cc78 100755
--- a/.scripts/conda_upload.sh
+++ b/.scripts/conda_upload.sh
@@ -9,7 +9,7 @@ mkdir ~/conda-bld
 conda config --set anaconda_upload no
 export CONDA_BLD_PATH=~/conda-bld
 
-export CIL_VERSION=3.0
+export CIL_VERSION=3.0.1
 $CONDA/bin/conda build conda-recipe . -c httomo
 
 # upload packages to conda
diff --git a/.scripts/conda_upload_lib.sh b/.scripts/conda_upload_lib.sh
new file mode 100755
index 0000000..6d5fa02
--- /dev/null
+++ b/.scripts/conda_upload_lib.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+
+PKG_NAME=libtomophantom
+USER=httomo-team
+OS=noarch
+CONDA_TOKEN=$(cat $HOME/.secrets/my_secret.json)
+
+mkdir ~/conda-bld
+conda config --set anaconda_upload no
+export CONDA_BLD_PATH=~/conda-bld
+
+export CIL_VERSION=3.0.1
+$CONDA/bin/conda build conda-recipe_library . -c httomo
+
+# upload packages to conda
+find $CONDA_BLD_PATH/$OS -name *.tar.bz2 | while read file
+do
+    echo $file
+    $CONDA/bin/anaconda -v --show-traceback --token $CONDA_TOKEN upload $file --force
+done

From 36505a86e97ff114025da2c49f08e496be97d983 Mon Sep 17 00:00:00 2001
From: dkazanc <dkazanc@hotmail.com>
Date: Mon, 12 Aug 2024 17:00:19 +0100
Subject: [PATCH 2/6] correcting ci's

---
 .github/workflows/libtomophantom_conda_upload.yml | 3 ---
 .github/workflows/tomophantom_conda_upload.yml    | 3 ---
 .scripts/conda_upload_lib.sh                      | 2 +-
 3 files changed, 1 insertion(+), 7 deletions(-)

diff --git a/.github/workflows/libtomophantom_conda_upload.yml b/.github/workflows/libtomophantom_conda_upload.yml
index 603433b..baf04db 100644
--- a/.github/workflows/libtomophantom_conda_upload.yml
+++ b/.github/workflows/libtomophantom_conda_upload.yml
@@ -13,9 +13,6 @@ jobs:
     steps:
       - name: Checkout repository code
         uses: actions/checkout@v4
-        with:
-          ref: "master"
-          fetch-depth: 0
 
       # setup Python 3.11
       - name: Setup Python 3.11
diff --git a/.github/workflows/tomophantom_conda_upload.yml b/.github/workflows/tomophantom_conda_upload.yml
index f857971..da22b87 100644
--- a/.github/workflows/tomophantom_conda_upload.yml
+++ b/.github/workflows/tomophantom_conda_upload.yml
@@ -13,9 +13,6 @@ jobs:
     steps:
       - name: Checkout repository code
         uses: actions/checkout@v4
-        with:
-          ref: "master"
-          fetch-depth: 0
 
       # setup Python 3.11
       - name: Setup Python 3.11
diff --git a/.scripts/conda_upload_lib.sh b/.scripts/conda_upload_lib.sh
index 6d5fa02..0bc3030 100755
--- a/.scripts/conda_upload_lib.sh
+++ b/.scripts/conda_upload_lib.sh
@@ -13,7 +13,7 @@ export CIL_VERSION=3.0.1
 $CONDA/bin/conda build conda-recipe_library . -c httomo
 
 # upload packages to conda
-find $CONDA_BLD_PATH/$OS -name *.tar.bz2 | while read file
+find $CONDA_BLD_PATH/$OS -name *.tar.bz2 | while read -r file
 do
     echo $file
     $CONDA/bin/anaconda -v --show-traceback --token $CONDA_TOKEN upload $file --force

From 5882ae39aa9c7dee0bd81f47794dddfbfa3fb215 Mon Sep 17 00:00:00 2001
From: dkazanc <dkazanc@hotmail.com>
Date: Mon, 12 Aug 2024 17:08:20 +0100
Subject: [PATCH 3/6] correcting ci's - 2

---
 .github/workflows/libtomophantom_conda_upload.yml | 8 ++++----
 .github/workflows/tomophantom_conda_upload.yml    | 8 ++++----
 .scripts/conda_upload.sh                          | 2 +-
 .scripts/conda_upload_lib.sh                      | 4 ++--
 4 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/libtomophantom_conda_upload.yml b/.github/workflows/libtomophantom_conda_upload.yml
index baf04db..b5ec6b0 100644
--- a/.github/workflows/libtomophantom_conda_upload.yml
+++ b/.github/workflows/libtomophantom_conda_upload.yml
@@ -14,11 +14,11 @@ jobs:
       - name: Checkout repository code
         uses: actions/checkout@v4
 
-      # setup Python 3.11
-      - name: Setup Python 3.11
-        uses: actions/setup-python@v2
+      # setup Python 3.10
+      - name: Setup Python 3.10
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: '3.10'
 
       - name: Install dependencies with Conda
         run: |
diff --git a/.github/workflows/tomophantom_conda_upload.yml b/.github/workflows/tomophantom_conda_upload.yml
index da22b87..c02849e 100644
--- a/.github/workflows/tomophantom_conda_upload.yml
+++ b/.github/workflows/tomophantom_conda_upload.yml
@@ -14,11 +14,11 @@ jobs:
       - name: Checkout repository code
         uses: actions/checkout@v4
 
-      # setup Python 3.11
-      - name: Setup Python 3.11
-        uses: actions/setup-python@v2
+      # setup Python 3.10
+      - name: Setup Python 3.10
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: '3.10'
 
       - name: Install dependencies with Conda
         run: |
diff --git a/.scripts/conda_upload.sh b/.scripts/conda_upload.sh
index f91cc78..0ce3760 100755
--- a/.scripts/conda_upload.sh
+++ b/.scripts/conda_upload.sh
@@ -13,7 +13,7 @@ export CIL_VERSION=3.0.1
 $CONDA/bin/conda build conda-recipe . -c httomo
 
 # upload packages to conda
-find $CONDA_BLD_PATH/$OS -name *.tar.bz2 | while read file
+find $CONDA_BLD_PATH/$OS -name '*.tar.bz2' | while read -r file
 do
     echo $file
     $CONDA/bin/anaconda -v --show-traceback --token $CONDA_TOKEN upload $file --force
diff --git a/.scripts/conda_upload_lib.sh b/.scripts/conda_upload_lib.sh
index 0bc3030..ff1e14b 100755
--- a/.scripts/conda_upload_lib.sh
+++ b/.scripts/conda_upload_lib.sh
@@ -2,7 +2,7 @@
 
 PKG_NAME=libtomophantom
 USER=httomo-team
-OS=noarch
+OS=linux-64
 CONDA_TOKEN=$(cat $HOME/.secrets/my_secret.json)
 
 mkdir ~/conda-bld
@@ -13,7 +13,7 @@ export CIL_VERSION=3.0.1
 $CONDA/bin/conda build conda-recipe_library . -c httomo
 
 # upload packages to conda
-find $CONDA_BLD_PATH/$OS -name *.tar.bz2 | while read -r file
+find $CONDA_BLD_PATH/$OS -name '*.tar.bz2' | while read -r file
 do
     echo $file
     $CONDA/bin/anaconda -v --show-traceback --token $CONDA_TOKEN upload $file --force

From e5b60e22eb28d93f170b239779b803a8bcc0a494 Mon Sep 17 00:00:00 2001
From: dkazanc <dkazanc@hotmail.com>
Date: Mon, 12 Aug 2024 17:11:59 +0100
Subject: [PATCH 4/6] correcting ci lib

---
 .github/workflows/tomophantom_conda_upload.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/tomophantom_conda_upload.yml b/.github/workflows/tomophantom_conda_upload.yml
index c02849e..5b44faa 100644
--- a/.github/workflows/tomophantom_conda_upload.yml
+++ b/.github/workflows/tomophantom_conda_upload.yml
@@ -23,6 +23,7 @@ jobs:
       - name: Install dependencies with Conda
         run: |
           $CONDA/bin/conda install -c conda-forge conda-build anaconda-client
+          $CONDA/bin/conda install --solver=classic conda-forge::conda-libmamba-solver conda-forge::libmamba conda-forge::libmambapy conda-forge::libarchive
           $CONDA/bin/conda update conda
           $CONDA/bin/conda update conda-build
           $CONDA/bin/conda list

From 103e8580e2d405202d49948c4d73917d5d1d8326 Mon Sep 17 00:00:00 2001
From: dkazanc <dkazanc@hotmail.com>
Date: Mon, 12 Aug 2024 17:16:00 +0100
Subject: [PATCH 5/6] correcting ci lib2

---
 .github/workflows/libtomophantom_conda_upload.yml | 1 +
 .github/workflows/tomophantom_conda_upload.yml    | 3 +--
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/libtomophantom_conda_upload.yml b/.github/workflows/libtomophantom_conda_upload.yml
index b5ec6b0..b0a2448 100644
--- a/.github/workflows/libtomophantom_conda_upload.yml
+++ b/.github/workflows/libtomophantom_conda_upload.yml
@@ -23,6 +23,7 @@ jobs:
       - name: Install dependencies with Conda
         run: |
           $CONDA/bin/conda install -c conda-forge conda-build anaconda-client
+          $CONDA/bin/conda install --solver=classic conda-forge::conda-libmamba-solver conda-forge::libmamba conda-forge::libmambapy conda-forge::libarchive
           $CONDA/bin/conda install -c conda-forge cmake
           $CONDA/bin/conda update conda
           $CONDA/bin/conda update conda-build
diff --git a/.github/workflows/tomophantom_conda_upload.yml b/.github/workflows/tomophantom_conda_upload.yml
index 5b44faa..2ef9eb5 100644
--- a/.github/workflows/tomophantom_conda_upload.yml
+++ b/.github/workflows/tomophantom_conda_upload.yml
@@ -22,8 +22,7 @@ jobs:
 
       - name: Install dependencies with Conda
         run: |
-          $CONDA/bin/conda install -c conda-forge conda-build anaconda-client
-          $CONDA/bin/conda install --solver=classic conda-forge::conda-libmamba-solver conda-forge::libmamba conda-forge::libmambapy conda-forge::libarchive
+          $CONDA/bin/conda install -c conda-forge conda-build anaconda-client          
           $CONDA/bin/conda update conda
           $CONDA/bin/conda update conda-build
           $CONDA/bin/conda list

From 51995b8bfaf1cc16262436d59d73c8aaf8fc2148 Mon Sep 17 00:00:00 2001
From: dkazanc <dkazanc@hotmail.com>
Date: Mon, 12 Aug 2024 17:20:43 +0100
Subject: [PATCH 6/6] bumping up ubuntus version

---
 .github/workflows/libtomophantom_conda_upload.yml | 2 +-
 .github/workflows/tomophantom_conda_upload.yml    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/libtomophantom_conda_upload.yml b/.github/workflows/libtomophantom_conda_upload.yml
index b0a2448..6556067 100644
--- a/.github/workflows/libtomophantom_conda_upload.yml
+++ b/.github/workflows/libtomophantom_conda_upload.yml
@@ -4,7 +4,7 @@ on: [push]
 
 jobs:
   build-linux:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     defaults:
       run:
diff --git a/.github/workflows/tomophantom_conda_upload.yml b/.github/workflows/tomophantom_conda_upload.yml
index 2ef9eb5..09007b6 100644
--- a/.github/workflows/tomophantom_conda_upload.yml
+++ b/.github/workflows/tomophantom_conda_upload.yml
@@ -4,7 +4,7 @@ on: [push]
 
 jobs:
   build-linux:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     defaults:
       run: