From 38dc630086c43b9808f315ae6feeee452526828c Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Fri, 22 Dec 2023 14:05:51 +0100
Subject: [PATCH] Implement pipreqs in CI (squashed)

---
 .github/workflows/lint-code.yml | 36 +++++++++++++++++++++++++++++++++
 requirements.txt                | 26 +++++++++++++++---------
 2 files changed, 53 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index a4914135..2ef3ef13 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -56,3 +56,39 @@ jobs:
       - name: mypy --> Static type checking
         # Configured in pyprojet.toml
         run: mypy **/*.py
+
+  # Use pipreqs to check for missing dependencies
+  pipreqs-check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Install pipreqs
+        run: pip install pipreqs
+      
+      - name: Install requirements
+        run: pip install -r requirements.txt
+
+      - name: Run pipreqs
+        run: pipreqs --savepath pipreqs.txt
+
+      - name: Compare requirements
+        run: |
+          # Extract and sort package names
+          awk '{print $1}' $1 | sort -u > "$1".compare
+          awk -F'==' '{print $1}' $2 | sort -u > "$2".compare
+
+          # Compare package lists
+          if cmp -s "$1".compare "$2".compare
+          then
+            echo "Requirements are the same"
+            exit 0
+          else
+            echo "Requirements are different"
+            exit 1
+          fi
diff --git a/requirements.txt b/requirements.txt
index 2ba779c9..f4dfdcb5 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,9 +1,17 @@
-CouchDB==1.2
-genologics==1.0.0
-google_api_python_client==2.111.0
-httplib2==0.22.0
-interop==1.3.1
-oauth2client==4.1.3
-pandas==2.1.4
-protobuf==4.25.1
-psycopg2==2.9.9
\ No newline at end of file
+CouchDB
+flowcell_parser @ git+https://github.com/SciLifeLab/flowcell_parser
+genologics
+google_api_python_client
+httplib2
+interop
+Markdown
+numpy
+oauth2client
+pandas
+protobuf
+psycopg2
+PyYAML
+Requests
+scilifelab_parsers @ git+https://github.com/SciLifeLab/scilifelab_parsers
+setuptools
+tabulate
\ No newline at end of file