From 1fbdd692e545a36bd5379f34c759a7fd94038894 Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 14:26:39 +0200
Subject: [PATCH 01/32] Update ci.yml

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index dd2dcdc..3cbb106 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -3,7 +3,7 @@ name: CI
 on: [push, pull_request]
 
 env:
-    SKIP: true
+    SKIP: false
 
 jobs:
   before_script:

From 0558e31ca20b32f735ba559f3e524d7a6eea7689 Mon Sep 17 00:00:00 2001
From: Andreas Piter <167966024+Andreas-Piter@users.noreply.github.com>
Date: Wed, 11 Sep 2024 15:46:12 +0200
Subject: [PATCH 02/32] Debug docs. Comment tests.

---
 .github/workflows/ci.yml | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3cbb106..4f029f8 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -55,7 +55,7 @@ jobs:
           unzip testdata.zip
           mv testdata tests/
           mamba list
-          make pytest
+          #make pytest
         shell: bash
 
       - name: create docs
@@ -206,6 +206,16 @@ jobs:
           mkdir -p public/images/
           mkdir -p public/coverage
           mkdir -p public/test_reports
+
+          ls -al docs/_build/html
+          # Copy command with checks if directories exist
+          if [ -d docs/_build/html ]; then
+              cp -r docs/_build/html/* public/doc/
+          else
+              echo "docs/_build/html does not exist"
+              exit 1
+          fi
+          
           cp -r docs/_build/html/* public/doc/
           cp -r htmlcov/* public/coverage/
           cp report.html public/test_reports/

From 0b6e2084dbfbbf43c3ad95473ea0a5292849231c Mon Sep 17 00:00:00 2001
From: Andreas Piter <167966024+Andreas-Piter@users.noreply.github.com>
Date: Wed, 11 Sep 2024 16:28:36 +0200
Subject: [PATCH 03/32] Comment test_install. Check directory content.

---
 .github/workflows/ci.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4f029f8..fc42630 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -168,6 +168,7 @@ jobs:
           python-version: '3.x'
 
       -   name: Install dependencies
+          if: false
           run: |
               source $HOME/miniconda/bin/activate
               mamba update -n base mamba conda
@@ -207,7 +208,7 @@ jobs:
           mkdir -p public/coverage
           mkdir -p public/test_reports
 
-          ls -al docs/_build/html
+          ls
           # Copy command with checks if directories exist
           if [ -d docs/_build/html ]; then
               cp -r docs/_build/html/* public/doc/

From 4aea27ce1ade5afdb722080079f7296ee0a2586a Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 17:16:25 +0200
Subject: [PATCH 04/32] download artifact before deploy

---
 .github/workflows/ci.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index fc42630..83a90c5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -198,6 +198,11 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: '3.x'
+      
+      - name: Download docs
+        uses: actions/download-artifact@v4
+        with:
+          name: docs
 
       - name: Deploy to GitHub Pages
         if: env.SKIP == 'false'

From c04b412c9d2d511112b6921ea98cd72a02f86291 Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 17:31:01 +0200
Subject: [PATCH 05/32] list docs/ docs/_build

---
 .github/workflows/ci.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 83a90c5..5f5a712 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -213,8 +213,10 @@ jobs:
           mkdir -p public/coverage
           mkdir -p public/test_reports
 
-          ls
-          # Copy command with checks if directories exist
+          # ls
+          ls docs/
+          ls docs/_build
+          Copy command with checks if directories exist
           if [ -d docs/_build/html ]; then
               cp -r docs/_build/html/* public/doc/
           else

From 0981ddccdd1d2c90838ba330f7a29e68e89823be Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 18:03:31 +0200
Subject: [PATCH 06/32] uncomment test_install

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5f5a712..53d62cf 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -168,7 +168,7 @@ jobs:
           python-version: '3.x'
 
       -   name: Install dependencies
-          if: false
+          # if: false
           run: |
               source $HOME/miniconda/bin/activate
               mamba update -n base mamba conda

From 915a8fe435197458e0be8dfa7f55c359c0a24bb8 Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 19:55:49 +0200
Subject: [PATCH 07/32] remove ci_temp_env directory

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

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 53d62cf..28424c6 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -47,6 +47,9 @@ jobs:
           conda init bash
           source ~/.bashrc
           mamba env remove --name ci_temp_env --yes || echo "Environment ci_temp_env does not exist"
+          # remove ci_temp_env directory
+          env_path=$(mamba info --envs | grep ci_temp_env | awk '{print $2}')
+          rm -rf $env_path
           conda create -n ci_temp_env --clone ci_env
           source activate ci_temp_env
           mamba install json5

From 7fc72bdd99793e15f74a29405e6c06abe59ef69c Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 19:58:01 +0200
Subject: [PATCH 08/32] comment test install

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 28424c6..2dd3ac4 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -171,7 +171,7 @@ jobs:
           python-version: '3.x'
 
       -   name: Install dependencies
-          # if: false
+          if: false
           run: |
               source $HOME/miniconda/bin/activate
               mamba update -n base mamba conda

From 025f2ea40cc222aed10801112b0581750a82d657 Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 20:04:39 +0200
Subject: [PATCH 09/32] remove ci_temp_env if it is a valid mamba env

---
 .github/workflows/ci.yml | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2dd3ac4..a99bf09 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -46,10 +46,14 @@ jobs:
         run: |
           conda init bash
           source ~/.bashrc
-          mamba env remove --name ci_temp_env --yes || echo "Environment ci_temp_env does not exist"
-          # remove ci_temp_env directory
-          env_path=$(mamba info --envs | grep ci_temp_env | awk '{print $2}')
-          rm -rf $env_path
+          # mamba env remove --name ci_temp_env --yes || echo "Environment ci_temp_env does not exist"
+          
+          if mamba info --envs | grep -q "ci_temp_env"; then
+            mamba env remove --name ci_temp_env --yes
+          else
+            echo "ci_temp_env is not a valid conda environment, skipping removal"
+          fi
+          
           conda create -n ci_temp_env --clone ci_env
           source activate ci_temp_env
           mamba install json5

From cf6428476d33252f2a71aab97ffbfac69a11e5c3 Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 20:09:17 +0200
Subject: [PATCH 10/32] remove ci_temp_env directory

---
 .github/workflows/ci.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a99bf09..0206318 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -50,9 +50,8 @@ jobs:
           
           if mamba info --envs | grep -q "ci_temp_env"; then
             mamba env remove --name ci_temp_env --yes
-          else
-            echo "ci_temp_env is not a valid conda environment, skipping removal"
           fi
+          rm -rf ~/.conda/envs/ci_temp_env
           
           conda create -n ci_temp_env --clone ci_env
           source activate ci_temp_env

From 8c8094638de30ca4932fab6e04aec9e82b9d7977 Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 20:23:23 +0200
Subject: [PATCH 11/32] skip sarvey test. download artifact to docs/_build/

---
 .github/workflows/ci.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 0206318..8914046 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -43,6 +43,7 @@ jobs:
           python-version: '3.x'
 
       - name: Run tests
+        if: false
         run: |
           conda init bash
           source ~/.bashrc
@@ -209,6 +210,7 @@ jobs:
         uses: actions/download-artifact@v4
         with:
           name: docs
+          path: docs/_build/
 
       - name: Deploy to GitHub Pages
         if: env.SKIP == 'false'

From 6eefa4f0f2bdac8247e3a4e7f2d36da4f48b74f7 Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 20:32:08 +0200
Subject: [PATCH 12/32] comment htmlcov and report.html.

---
 .github/workflows/ci.yml | 15 ++-------------
 1 file changed, 2 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8914046..5173d11 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -220,21 +220,10 @@ jobs:
           mkdir -p public/images/
           mkdir -p public/coverage
           mkdir -p public/test_reports
-
-          # ls
-          ls docs/
-          ls docs/_build
-          Copy command with checks if directories exist
-          if [ -d docs/_build/html ]; then
-              cp -r docs/_build/html/* public/doc/
-          else
-              echo "docs/_build/html does not exist"
-              exit 1
-          fi
           
           cp -r docs/_build/html/* public/doc/
-          cp -r htmlcov/* public/coverage/
-          cp report.html public/test_reports/
+          # cp -r htmlcov/* public/coverage/
+          # cp report.html public/test_reports/
           ls -al public
           ls -al public/doc
           ls -al public/coverage

From 43cba41709e6c3e3b013c731c4d69e1936f7949b Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 20:36:57 +0200
Subject: [PATCH 13/32] comment ls public/*

---
 .github/workflows/ci.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5173d11..20961e5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -224,10 +224,10 @@ jobs:
           cp -r docs/_build/html/* public/doc/
           # cp -r htmlcov/* public/coverage/
           # cp report.html public/test_reports/
-          ls -al public
+          # ls -al public
           ls -al public/doc
-          ls -al public/coverage
-          ls -al public/test_reports
+          # ls -al public/coverage
+          # ls -al public/test_reports
         shell: bash
 
       - name: Upload to GitHub Pages

From 4fbf3f9e4cfb56a5bdb91c00927be32fdc8f3998 Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 20:40:39 +0200
Subject: [PATCH 14/32] download docs artifact to /docs/_build/html

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 20961e5..d8d024b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -210,7 +210,7 @@ jobs:
         uses: actions/download-artifact@v4
         with:
           name: docs
-          path: docs/_build/
+          path: docs/_build/html/
 
       - name: Deploy to GitHub Pages
         if: env.SKIP == 'false'

From 21e46ec80f46ae2c6b13dce8315e2e5381770d02 Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 21:06:35 +0200
Subject: [PATCH 15/32] add permissions contents write to allow pushes to
 gh-pages

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

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d8d024b..c25dcb1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -2,6 +2,9 @@ name: CI
 
 on: [push, pull_request]
 
+permissions:
+  contents: write
+
 env:
     SKIP: false
 

From 1f0d53e9e48ab7b6d6c70d161019e7c9ee6e4241 Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 21:13:26 +0200
Subject: [PATCH 16/32] fix doc to docs

---
 .github/workflows/ci.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c25dcb1..29c73b9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -219,16 +219,16 @@ jobs:
         if: env.SKIP == 'false'
         run: |
           rm -rf public
-          mkdir -p public/doc
+          mkdir -p public/docs
           mkdir -p public/images/
           mkdir -p public/coverage
           mkdir -p public/test_reports
           
-          cp -r docs/_build/html/* public/doc/
+          cp -r docs/_build/html/* public/docs/
           # cp -r htmlcov/* public/coverage/
           # cp report.html public/test_reports/
           # ls -al public
-          ls -al public/doc
+          ls -al public/docs
           # ls -al public/coverage
           # ls -al public/test_reports
         shell: bash

From 361f93557b5a9f6c5abf2825bfbf8127bdb7f4cb Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 21:48:03 +0200
Subject: [PATCH 17/32] add baseurl to conf.py

---
 docs/conf.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/docs/conf.py b/docs/conf.py
index 865df13..49dceea 100755
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -229,6 +229,9 @@ def setup(app):
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'sarveydoc'
 
+# baseurel
+html_baseurl = 'https://luhipi.github.io/sarvey/docs/'
+
 
 # -- Options for LaTeX output ------------------------------------------
 

From 06c1514bbb860cd838d3afd0d45125b5844600f6 Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 21:58:04 +0200
Subject: [PATCH 18/32] remove baseurl from conf.py

---
 docs/conf.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index 49dceea..865df13 100755
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -229,9 +229,6 @@ def setup(app):
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'sarveydoc'
 
-# baseurel
-html_baseurl = 'https://luhipi.github.io/sarvey/docs/'
-
 
 # -- Options for LaTeX output ------------------------------------------
 

From 2dcd38fe18d25dc67aa5a76185b9a8f8ad68e601 Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 22:09:53 +0200
Subject: [PATCH 19/32] uncomment public/*

---
 .github/workflows/ci.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 29c73b9..1ff2561 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -225,12 +225,12 @@ jobs:
           mkdir -p public/test_reports
           
           cp -r docs/_build/html/* public/docs/
-          # cp -r htmlcov/* public/coverage/
-          # cp report.html public/test_reports/
-          # ls -al public
+          cp -r htmlcov/* public/coverage/
+          cp report.html public/test_reports/
+          ls -al public
           ls -al public/docs
-          # ls -al public/coverage
-          # ls -al public/test_reports
+          ls -al public/coverage
+          ls -al public/test_reports
         shell: bash
 
       - name: Upload to GitHub Pages

From c827a2f67bc973c34dd96af127d0c95db3a7802b Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 22:18:34 +0200
Subject: [PATCH 20/32] download coverage and report artifact

---
 .github/workflows/ci.yml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1ff2561..8ff94d8 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -215,6 +215,18 @@ jobs:
           name: docs
           path: docs/_build/html/
 
+      - name: Download coverage report
+        uses: actions/download-artifact@v4
+        with:
+          name: coverage-report
+          path: htmlcov/
+
+      - name: Download report.html
+        uses: actions/download-artifact@v4
+        with:
+          name: test-report
+          path: report.html
+
       - name: Deploy to GitHub Pages
         if: env.SKIP == 'false'
         run: |

From 64a167121b0919b7d5e6a2a2430df3595bdd9157 Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 22:28:19 +0200
Subject: [PATCH 21/32] uncomment pytest

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8ff94d8..89f52fd 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -65,7 +65,7 @@ jobs:
           unzip testdata.zip
           mv testdata tests/
           mamba list
-          #make pytest
+          make pytest
         shell: bash
 
       - name: create docs

From c74834a1fbfe062762387a736a4f0ce9eada2c78 Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 22:33:53 +0200
Subject: [PATCH 22/32] run test_srarvey

---
 .github/workflows/ci.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 89f52fd..4c6b41f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -46,7 +46,6 @@ jobs:
           python-version: '3.x'
 
       - name: Run tests
-        if: false
         run: |
           conda init bash
           source ~/.bashrc

From 87cd5753e92c82a945d7b4ded51b7e00c4929db6 Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Wed, 11 Sep 2024 22:50:28 +0200
Subject: [PATCH 23/32] download report.html artifact

---
 .github/workflows/ci.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4c6b41f..06ec768 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -224,7 +224,6 @@ jobs:
         uses: actions/download-artifact@v4
         with:
           name: test-report
-          path: report.html
 
       - name: Deploy to GitHub Pages
         if: env.SKIP == 'false'

From 3a160da9befa0a14f8e4fc3e3ca6f069f502183f Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Thu, 12 Sep 2024 11:10:17 +0200
Subject: [PATCH 24/32] update README.rst with links to GitHub pages

---
 README.rst | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/README.rst b/README.rst
index 0ec0392..486466b 100644
--- a/README.rst
+++ b/README.rst
@@ -10,21 +10,21 @@ Open-source InSAR time series analysis software developed within the project SAR
 Documentation
 -------------
 The documentation with installation instructions, processing steps, and examples with a demo dataset can be found at:
-https://ipi-sar4infra.projektpages.uni-h.de/timeseries/doc/
+https://luhipi.github.io/sarvey/docs/
 
 
 
 Status
 ------
 
-.. image:: https://gitlab.projekt.uni-hannover.de/ipi-sar4infra/timeseries/badges/main/pipeline.svg
-        :target: https://gitlab.projekt.uni-hannover.de/ipi-sar4infra/timeseries/-/pipelines
+.. image:: https://github.com/luhipi/sarvey/actions/workflows/ci.yml/badge.svg
+        :target: https://github.com/luhipi/sarvey/actions
         :alt: Pipelines
 .. image:: https://gitlab.projekt.uni-hannover.de/ipi-sar4infra/timeseries/badges/main/coverage.svg
         :target: https://ipi-sar4infra.projektpages.uni-h.de/timeseries/coverage/
         :alt: Coverage
-.. image:: https://img.shields.io/static/v1?label=Documentation&message=GitLab%20Pages&color=orange
-        :target: https://ipi-sar4infra.projektpages.uni-h.de/timeseries/doc/
+.. image:: https://img.shields.io/static/v1?label=Documentation&message=GitHub%20Pages&color=blue
+        :target: https://luhipi.github.io/sarvey/docs/
         :alt: Documentation
 .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.12544131.svg
         :target: https://doi.org/10.5281/zenodo.12544131
@@ -188,8 +188,8 @@ This package was created with Cookiecutter_ and the `fernlab/cookiecutter-pypack
 
 .. _Cookiecutter: https://github.com/audreyr/cookiecutter
 .. _`fernlab/cookiecutter-pypackage`: https://github.com/fernlab/cookiecutter-pypackage
-.. _coverage: https://ipi-sar4infra.projektpages.uni-h.de/timeseries/coverage/
-.. _pytest: https://ipi-sar4infra.projektpages.uni-h.de/timeseries/test_reports/report.html
+.. _coverage: https://luhipi.github.io/sarvey/coverage/
+.. _pytest: https://luhipi.github.io/sarvey/test_reports/report.html
 .. _processing: docs/processing.html
 .. _`installation instruction`: docs/installation.html
 .. _MiaplPy: https://github.com/insarlab/MiaplPy

From 0882b41ee6306bd73435505416282fb4aa5b2724 Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Thu, 12 Sep 2024 13:33:27 +0200
Subject: [PATCH 25/32] revert mamba env remove

---
 .github/workflows/ci.yml | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 06ec768..dc04b70 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -49,12 +49,7 @@ jobs:
         run: |
           conda init bash
           source ~/.bashrc
-          # mamba env remove --name ci_temp_env --yes || echo "Environment ci_temp_env does not exist"
-          
-          if mamba info --envs | grep -q "ci_temp_env"; then
-            mamba env remove --name ci_temp_env --yes
-          fi
-          rm -rf ~/.conda/envs/ci_temp_env
+          mamba env remove --name ci_temp_env --yes || echo "Environment ci_temp_env does not exist"
           
           conda create -n ci_temp_env --clone ci_env
           source activate ci_temp_env

From 9e5f80c43a3d3ff8c7c6bebc32fc0062ed81410f Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Thu, 12 Sep 2024 13:54:42 +0200
Subject: [PATCH 26/32] revert install dependencies

---
 .github/workflows/ci.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index dc04b70..4645be0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -172,7 +172,6 @@ jobs:
           python-version: '3.x'
 
       -   name: Install dependencies
-          if: false
           run: |
               source $HOME/miniconda/bin/activate
               mamba update -n base mamba conda

From 5501af57b99bb6c63ac9c2562c5db73060cbd005 Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Thu, 12 Sep 2024 13:55:53 +0200
Subject: [PATCH 27/32] remove coverage badge from README.rst

---
 README.rst | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/README.rst b/README.rst
index 486466b..24b61a1 100644
--- a/README.rst
+++ b/README.rst
@@ -20,9 +20,6 @@ Status
 .. image:: https://github.com/luhipi/sarvey/actions/workflows/ci.yml/badge.svg
         :target: https://github.com/luhipi/sarvey/actions
         :alt: Pipelines
-.. image:: https://gitlab.projekt.uni-hannover.de/ipi-sar4infra/timeseries/badges/main/coverage.svg
-        :target: https://ipi-sar4infra.projektpages.uni-h.de/timeseries/coverage/
-        :alt: Coverage
 .. image:: https://img.shields.io/static/v1?label=Documentation&message=GitHub%20Pages&color=blue
         :target: https://luhipi.github.io/sarvey/docs/
         :alt: Documentation

From 3ab6ee9cc6af388966e7a3bfdc0b5839108b77ef Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Thu, 12 Sep 2024 14:44:49 +0200
Subject: [PATCH 28/32] update processing and installation links in README.rst

---
 README.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.rst b/README.rst
index 24b61a1..b745bff 100644
--- a/README.rst
+++ b/README.rst
@@ -187,8 +187,8 @@ This package was created with Cookiecutter_ and the `fernlab/cookiecutter-pypack
 .. _`fernlab/cookiecutter-pypackage`: https://github.com/fernlab/cookiecutter-pypackage
 .. _coverage: https://luhipi.github.io/sarvey/coverage/
 .. _pytest: https://luhipi.github.io/sarvey/test_reports/report.html
-.. _processing: docs/processing.html
-.. _`installation instruction`: docs/installation.html
+.. _processing: https://luhipi.github.io/sarvey/docs/processing.html
+.. _`installation instruction`: https://luhipi.github.io/sarvey/docs/installation.html
 .. _MiaplPy: https://github.com/insarlab/MiaplPy
 .. _ISCE: https://github.com/isce-framework/isce2
 .. _SNAP: https://step.esa.int/main/toolboxes/snap

From fe644985d281964dd24de4e3394b814712a592eb Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Thu, 12 Sep 2024 14:59:36 +0200
Subject: [PATCH 29/32] update links in README.rst

---
 README.rst | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/README.rst b/README.rst
index b745bff..a0645aa 100644
--- a/README.rst
+++ b/README.rst
@@ -86,12 +86,12 @@ SARvey is a command-line-based software. The major steps for running SARvey are
   The software requires a coregistered stack of SLC and the related geometry information in the MiaplPy_  data format.
   The coregistered stack of SLC can be created using an InSAR processor. Currently MiaplPy_ only supports ISCE_. Support for GAMMA and SNAP_ is planned for future.
   After creating the coregistered stack of SLC, run the "load_data" step from Miaplpy_ to create the "inputs" directory which contains "slcStack.h5" and "geometryRadar.h5".
-  Details are explained in the `Preparation <preparation.html>`_ section
+  Details are explained in the preparation_ section
 
 
 * **Time series analysis**
 
-  Time series analysis is performed using `sarvey`. It consists of 5 steps (steps 0 to 4). The details of each step are explained in `processing steps <processing.html#processing-steps-for-two-step-unwrapping-workflow>`_. The processing parameters are handled in a json config file. Visualization and export are handled by `sarvey_plot` and `sarvey_export` packages. Below are the major steps:
+  Time series analysis is performed using `sarvey`. It consists of 5 steps (steps 0 to 4). The details of each step are explained in `processing steps <_processing#processing-steps-for-two-step-unwrapping-workflow>`_. The processing parameters are handled in a json config file. Visualization and export are handled by `sarvey_plot` and `sarvey_export` packages. Below are the major steps:
 
   * Go to your working directory:
 
@@ -113,7 +113,7 @@ SARvey is a command-line-based software. The major steps for running SARvey are
 
          sarvey -f config.json 0 4
 
-    Different processing steps are explained `here <processing.html>`_.
+    Different processing steps are explained `here <_processing>`_.
 
   * Plot the resulting displacement time series:
 
@@ -152,10 +152,9 @@ You can run each component in the command line with "-h" argument for more infor
 
 **SARvey** supports two processing schemes:
 
-* `Two-step unwrapping <processing.html#processing-steps-for-two-step-unwrapping-workflow>`_ with atmospheric correction (default).
-
-* `One-step unwrapping <processing.html#processing-steps-for-one-step-unwrapping-workflow>`_ for a small area.
+* `Two-step unwrapping <_processing#processing-steps-for-two-step-unwrapping-workflow>`_ with atmospheric correction (default).
 
+* `One-step unwrapping <_processing#processing-steps-for-one-step-unwrapping-workflow>`_ for a small area.
 
 History / Changelog
 -------------------
@@ -188,6 +187,7 @@ This package was created with Cookiecutter_ and the `fernlab/cookiecutter-pypack
 .. _coverage: https://luhipi.github.io/sarvey/coverage/
 .. _pytest: https://luhipi.github.io/sarvey/test_reports/report.html
 .. _processing: https://luhipi.github.io/sarvey/docs/processing.html
+.. _preparation: https://luhipi.github.io/sarvey/docs/preparation.html
 .. _`installation instruction`: https://luhipi.github.io/sarvey/docs/installation.html
 .. _MiaplPy: https://github.com/insarlab/MiaplPy
 .. _ISCE: https://github.com/isce-framework/isce2

From 6c84a8b763ae4f7ddd79a095ef1a99d16d996cfa Mon Sep 17 00:00:00 2001
From: mahmud1 <mahmud1@users.noreply.github.com>
Date: Thu, 12 Sep 2024 15:14:35 +0200
Subject: [PATCH 30/32] update links in Readme.rst

---
 README.rst | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/README.rst b/README.rst
index a0645aa..13617b2 100644
--- a/README.rst
+++ b/README.rst
@@ -91,7 +91,7 @@ SARvey is a command-line-based software. The major steps for running SARvey are
 
 * **Time series analysis**
 
-  Time series analysis is performed using `sarvey`. It consists of 5 steps (steps 0 to 4). The details of each step are explained in `processing steps <_processing#processing-steps-for-two-step-unwrapping-workflow>`_. The processing parameters are handled in a json config file. Visualization and export are handled by `sarvey_plot` and `sarvey_export` packages. Below are the major steps:
+  Time series analysis is performed using `sarvey`. It consists of 5 steps (steps 0 to 4). The details of each step are explained in `processing steps`_. The processing parameters are handled in a json config file. Visualization and export are handled by `sarvey_plot` and `sarvey_export` packages. Below are the major steps:
 
   * Go to your working directory:
 
@@ -113,7 +113,7 @@ SARvey is a command-line-based software. The major steps for running SARvey are
 
          sarvey -f config.json 0 4
 
-    Different processing steps are explained `here <_processing>`_.
+    Different processing steps are explained in `processing`_ section.
 
   * Plot the resulting displacement time series:
 
@@ -152,15 +152,15 @@ You can run each component in the command line with "-h" argument for more infor
 
 **SARvey** supports two processing schemes:
 
-* `Two-step unwrapping <_processing#processing-steps-for-two-step-unwrapping-workflow>`_ with atmospheric correction (default).
+* `Two-step unwrapping`_ with atmospheric correction (default).
 
-* `One-step unwrapping <_processing#processing-steps-for-one-step-unwrapping-workflow>`_ for a small area.
+* `One-step unwrapping`_ for a small area.
 
 History / Changelog
 -------------------
 
 You can find the protocol of recent changes in the **SARvey** package
-`here <HISTORY.rst>`__.
+`history`_.
 
 We follow the principle of semantic versioning.
 The version number is structured as follows: MAJOR.MINOR.PATCH.
@@ -187,8 +187,12 @@ This package was created with Cookiecutter_ and the `fernlab/cookiecutter-pypack
 .. _coverage: https://luhipi.github.io/sarvey/coverage/
 .. _pytest: https://luhipi.github.io/sarvey/test_reports/report.html
 .. _processing: https://luhipi.github.io/sarvey/docs/processing.html
+.. _`processing steps`: https://luhipi.github.io/sarvey/docs/processing.html#processing-steps-for-two-step-unwrapping-workflow
 .. _preparation: https://luhipi.github.io/sarvey/docs/preparation.html
+.. _`Two-step unwrapping`: https://luhipi.github.io/sarvey/docs/processing.html#processing-steps-for-two-step-unwrapping-workflow
+.. _`One-step unwrapping`: https://luhipi.github.io/sarvey/docs/processing.html#processing-steps-for-one-step-unwrapping-workflow
 .. _`installation instruction`: https://luhipi.github.io/sarvey/docs/installation.html
+.. _`history`: https://luhipi.github.io/sarvey/docs/history.html
 .. _MiaplPy: https://github.com/insarlab/MiaplPy
 .. _ISCE: https://github.com/isce-framework/isce2
 .. _SNAP: https://step.esa.int/main/toolboxes/snap

From 27c155add15f0cf70caf3b9cee87dbcea41243ce Mon Sep 17 00:00:00 2001
From: mahmud1 <mahmud1@users.noreply.github.com>
Date: Thu, 12 Sep 2024 15:16:05 +0200
Subject: [PATCH 31/32] update paper information in Readme.rst

---
 README.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index 13617b2..80b6e61 100644
--- a/README.rst
+++ b/README.rst
@@ -50,7 +50,7 @@ If you use **SARvey** in your research, please cite the following.
 
 1. The paper describing the methodology:
 
-   Piter, A., Haghshenas Haghighi, M., Motagh, M.(2024). An in-depth study on Sentinel-1 InSAR for transport infrastructure monitoring. PFG - Journal of Photogrammetry, Remote Sensing and Geoinformation Science. (paper currently under review).
+   Piter, A., Haghshenas Haghighi, M., Motagh, M.(2024). Challenges and Opportunities of Sentinel-1 InSAR for Transport Infrastructure Monitoring. PFG - Journal of Photogrammetry, Remote Sensing and Geoinformation Science. (paper in press).
 
 2. The software itself. Please specify the version you use:
 

From 6fdc56f7bd74482b5bf7b2c1519c8ee868079572 Mon Sep 17 00:00:00 2001
From: Mahmud Haghighi <mahmud1@users.noreply.github.com>
Date: Thu, 12 Sep 2024 17:28:08 +0200
Subject: [PATCH 32/32] update paper in processing.rst

---
 docs/processing.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/processing.rst b/docs/processing.rst
index 128a826..0423bdf 100644
--- a/docs/processing.rst
+++ b/docs/processing.rst
@@ -325,7 +325,7 @@ Since the densification step is not performed, you should reduce the coherence t
 Literature
 ----------
 
-* Piter, A., Haghshenas Haghighi, M., Motagh, M.(2024). An in-depth study on Sentinel-1 InSAR for transport infrastructure monitoring. PFG - Journal of Photogrammetry, Remote Sensing and Geoinformation Science. (paper currently under review).
+* Piter, A., Haghshenas Haghighi, M., Motagh, M.(2024). Challenges and Opportunities of Sentinel-1 InSAR for Transport Infrastructure Monitoring. PFG - Journal of Photogrammetry, Remote Sensing and Geoinformation Science. (paper in press).
 
 * Zhao F, Mallorqui JJ (2019). A Temporal Phase Coherence Estimation Algorithm and Its Application on DInSAR Pixel Selection. IEEE Transactions on Geoscience and Remote Sensing 57(11):8350–8361, DOI 10.1109/TGRS.2019.2920536