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Merged
Vasilije1990 merged 38 commits into from
Dec 11, 2024
Merged

Added basic profiling #255

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39c2106
Added basic profiling
Vasilije1990 Dec 4, 2024
a935940
Added basic profiling
Vasilije1990 Dec 4, 2024
7e66d50
Added basic profiling
Vasilije1990 Dec 4, 2024
df7bbfe
Added basic profiling
Vasilije1990 Dec 4, 2024
d589255
Added basic profiling
Vasilije1990 Dec 4, 2024
94688ed
Added basic profiling
Vasilije1990 Dec 4, 2024
6171cd7
Added basic profiling
Vasilije1990 Dec 4, 2024
bba32aa
Added basic profiling
Vasilije1990 Dec 4, 2024
a904b8d
Added basic profiling
Vasilije1990 Dec 4, 2024
bdef152
Added basic profiling
Vasilije1990 Dec 4, 2024
e2539cd
Added basic profiling
Vasilije1990 Dec 4, 2024
6ab427e
Added basic profiling
Vasilije1990 Dec 4, 2024
fa60827
Added basic profiling
Vasilije1990 Dec 4, 2024
32ca751
Added basic profiling
Vasilije1990 Dec 4, 2024
d523f71
Added basic profiling
Vasilije1990 Dec 4, 2024
c2896f3
Added basic profiling
Vasilije1990 Dec 4, 2024
e178d38
Added basic profiling
Vasilije1990 Dec 4, 2024
21c7b8e
Bump release version
Vasilije1990 Dec 4, 2024
54b8844
Bump release version
Vasilije1990 Dec 4, 2024
692770c
Bump release version
Vasilije1990 Dec 4, 2024
2df1eb6
Bump release version
Vasilije1990 Dec 4, 2024
8d1936f
Bump release version
Vasilije1990 Dec 4, 2024
f37d96d
Bump release version
Vasilije1990 Dec 4, 2024
cc43a8c
Bump release version
Vasilije1990 Dec 4, 2024
cf51555
Bump release version
Vasilije1990 Dec 4, 2024
d2fccc1
Bump release version
Vasilije1990 Dec 4, 2024
a96daef
Bump release version
Vasilije1990 Dec 4, 2024
316f2f3
Merge branch 'main' into COG-698
Vasilije1990 Dec 5, 2024
0268df2
Merge branch 'main' into COG-698
borisarzentar Dec 6, 2024
ea879b2
Merge branch 'main' into COG-698
borisarzentar Dec 8, 2024
b397f9e
Merge branch 'main' into COG-698
borisarzentar Dec 9, 2024
c431e7c
Update profiling.yaml
Vasilije1990 Dec 10, 2024
5609bbc
removed issues
Vasilije1990 Dec 11, 2024
0e68019
fix
Vasilije1990 Dec 11, 2024
0f0e34e
Merge branch 'main' into COG-698
Vasilije1990 Dec 11, 2024
7cc5607
fix
Vasilije1990 Dec 11, 2024
4dac950
Merge remote-tracking branch 'origin/COG-698' into COG-698
Vasilije1990 Dec 11, 2024
9a9ea75
Fix neo4j
Vasilije1990 Dec 11, 2024
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137 changes: 137 additions & 0 deletions .github/workflows/profiling.yaml
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@@ -0,0 +1,137 @@
name: test | profiling

on:
push
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@coderabbitai coderabbitai bot Dec 4, 2024 •
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⚠️ Potential issue

Fix workflow trigger configuration

The current trigger configuration will fail because:

  1. The workflow requires pull request context for base/head SHA comparison
  2. Running on all pushes is inefficient and will fail for non-PR pushes

Update the trigger configuration:

on:
-  push
+  pull_request:
+    types: [opened, synchronize]
+    paths:
+      - 'cognee/api/v1/cognify/code_graph_pipeline.py'
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Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
on:
push
on:
pull_request:
types: [opened, synchronize]
paths:
- 'cognee/api/v1/cognify/code_graph_pipeline.py'

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@borisarzentar borisarzentar Dec 6, 2024

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@Vasilije1990 coderabbit has a good point here.

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Seems like the humans are having a chat. I'll hop back into my burrow for now. If you need me again, just tag @coderabbitai in a new comment, and I'll come hopping out!

jobs:
profiler:
runs-on: ubuntu-latest

steps:
# Checkout the code from the repository with full history
- name: Checkout code
uses: actions/checkout@v4
with:
fetch-depth: 0 # Fetch all history so we can checkout any commit

- name: Check if the sender is a maintainer
id: check_permissions
uses: actions/github-script@v6
with:
script: |
const sender = context.payload.sender.login;
const { data: membership } = await github.rest.orgs.getMembershipForUser({
org: context.repo.owner,
username: sender,
}).catch(() => ({ data: { role: null } }));
return membership.role;
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

- name: Set is_maintainer variable
run: |
echo "is_maintainer=${{ steps.check_permissions.outputs.result == 'admin' || steps.check_permissions.outputs.result == 'maintainer' }}" >> $GITHUB_ENV

- name: Stop if not a maintainer
if: env.is_maintainer != 'true'
run: |
echo "User ${{ github.event.sender.login }} is not a maintainer. Exiting."
exit 0 # Use exit 0 to mark the job as successful but stop execution
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🛠️ Refactor suggestion

Improve shell script security and error handling

The maintainer check implementation has potential security issues:

 - name: Set is_maintainer variable
   run: |
-    echo "is_maintainer=${{ steps.check_permissions.outputs.result == 'admin' || steps.check_permissions.outputs.result == 'maintainer' }}" >> $GITHUB_ENV
+    is_maintainer="${{ steps.check_permissions.outputs.result == 'admin' || steps.check_permissions.outputs.result == 'maintainer' }}"
+    echo "is_maintainer=${is_maintainer}" >> "$GITHUB_ENV"

 - name: Stop if not a maintainer
   if: env.is_maintainer != 'true'
   run: |
+    echo "::warning::Profiling skipped - User ${{ github.event.sender.login }} is not a maintainer"
     echo "User ${{ github.event.sender.login }} is not a maintainer. Exiting."
     exit 0
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
- name: Set is_maintainer variable
run: |
echo "is_maintainer=${{ steps.check_permissions.outputs.result == 'admin' || steps.check_permissions.outputs.result == 'maintainer' }}" >> $GITHUB_ENV
- name: Stop if not a maintainer
if: env.is_maintainer != 'true'
run: |
echo "User ${{ github.event.sender.login }} is not a maintainer. Exiting."
exit 0 # Use exit 0 to mark the job as successful but stop execution
- name: Set is_maintainer variable
run: |
is_maintainer="${{ steps.check_permissions.outputs.result == 'admin' || steps.check_permissions.outputs.result == 'maintainer' }}"
echo "is_maintainer=${is_maintainer}" >> "$GITHUB_ENV"
- name: Stop if not a maintainer
if: env.is_maintainer != 'true'
run: |
echo "::warning::Profiling skipped - User ${{ github.event.sender.login }} is not a maintainer"
echo "User ${{ github.event.sender.login }} is not a maintainer. Exiting."
exit 0 # Use exit 0 to mark the job as successful but stop execution
🧰 Tools
🪛 actionlint (1.7.4)

35-35: shellcheck reported issue in this script: SC2086:info:1:140: Double quote to prevent globbing and word splitting

(shellcheck)


# Set up Python environment
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: '3.10'

- name: Install Poetry
uses: snok/[email protected]
with:
virtualenvs-create: true
virtualenvs-in-project: true
installer-parallel: true

- name: Install dependencies
run: |
poetry install --no-interaction --all-extras
poetry run pip install pyinstrument
Comment on lines +46 to +56
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🛠️ Refactor suggestion

Improve dependency management security and efficiency

The current setup could be more secure and efficient:

 - name: Install Poetry
   uses: snok/[email protected]
   with:
     virtualenvs-create: true
     virtualenvs-in-project: true
     installer-parallel: true
+    version: 1.7.1  # Pin to specific version

 - name: Install dependencies
   run: |
+    # Verify poetry.lock is in sync
+    poetry lock --check
-    poetry install --no-interaction --all-extras
+    # Install only needed dependencies
+    poetry install --no-interaction --only main,dev
     poetry run pip install pyinstrument
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
- name: Install Poetry
uses: snok/[email protected]
with:
virtualenvs-create: true
virtualenvs-in-project: true
installer-parallel: true
- name: Install dependencies
run: |
poetry install --no-interaction --all-extras
poetry run pip install pyinstrument
- name: Install Poetry
uses: snok/[email protected]
with:
virtualenvs-create: true
virtualenvs-in-project: true
installer-parallel: true
version: 1.7.1 # Pin to specific version
- name: Install dependencies
run: |
# Verify poetry.lock is in sync
poetry lock --check
# Install only needed dependencies
poetry install --no-interaction --only main,dev
poetry run pip install pyinstrument



# Set environment variables for SHAs
- name: Set environment variables
run: |
echo "BASE_SHA=${{ github.event.pull_request.base.sha }}" >> $GITHUB_ENV
echo "HEAD_SHA=${{ github.event.pull_request.head.sha }}" >> $GITHUB_ENV

Comment on lines +60 to +64
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⚠️ Potential issue

Improve environment variables setup

The current setup lacks validation and has potential shell scripting issues.

     - name: Set environment variables
       run: |
+        if [[ -z "${{ github.event.pull_request }}" ]]; then
+          echo "Error: No pull request context found"
+          exit 1
+        fi
-        echo "BASE_SHA=${{ github.event.pull_request.base.sha }}" >> $GITHUB_ENV
-        echo "HEAD_SHA=${{ github.event.pull_request.head.sha }}" >> $GITHUB_ENV
+        echo "BASE_SHA=${{ github.event.pull_request.base.sha }}" >> "$GITHUB_ENV"
+        echo "HEAD_SHA=${{ github.event.pull_request.head.sha }}" >> "$GITHUB_ENV"
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
- name: Set environment variables
run: |
echo "BASE_SHA=${{ github.event.pull_request.base.sha }}" >> $GITHUB_ENV
echo "HEAD_SHA=${{ github.event.pull_request.head.sha }}" >> $GITHUB_ENV
- name: Set environment variables
run: |
if [[ -z "${{ github.event.pull_request }}" ]]; then
echo "Error: No pull request context found"
exit 1
fi
echo "BASE_SHA=${{ github.event.pull_request.base.sha }}" >> "$GITHUB_ENV"
echo "HEAD_SHA=${{ github.event.pull_request.head.sha }}" >> "$GITHUB_ENV"
🧰 Tools
🪛 actionlint (1.7.4)

37-37: shellcheck reported issue in this script: SC2086:info:1:62: Double quote to prevent globbing and word splitting

(shellcheck)

37-37: shellcheck reported issue in this script: SC2086:info:2:62: Double quote to prevent globbing and word splitting

(shellcheck)

# Run profiler on the base branch
- name: Run profiler on base branch
env:
BASE_SHA: ${{ env.BASE_SHA }}
run: |
echo "Profiling the base branch for code_graph_pipeline.py"
echo "Checking out base SHA: $BASE_SHA"
git checkout $BASE_SHA
echo "This is the working directory: $PWD"
# Ensure the script is executable
chmod +x cognee/api/v1/cognify/code_graph_pipeline.py
# Run Scalene
poetry run pyinstrument --renderer json -o base_results.json cognee/api/v1/cognify/code_graph_pipeline.py

# Run profiler on head branch
- name: Run profiler on head branch
env:
HEAD_SHA: ${{ env.HEAD_SHA }}
run: |
echo "Profiling the head branch for code_graph_pipeline.py"
echo "Checking out head SHA: $HEAD_SHA"
git checkout $HEAD_SHA
echo "This is the working directory: $PWD"
# Ensure the script is executable
chmod +x cognee/api/v1/cognify/code_graph_pipeline.py
# Run Scalene
poetry run pyinstrument --renderer json -o head_results.json cognee/api/v1/cognify/code_graph_pipeline.py

# Compare profiling results
- name: Compare profiling results
run: |
python -c '
import json
try:
with open("base_results.json") as f:
base = json.load(f)
with open("head_results.json") as f:
head = json.load(f)
cpu_diff = head.get("total_cpu_samples_python", 0) - base.get("total_cpu_samples_python", 0)
memory_diff = head.get("malloc_samples", 0) - base.get("malloc_samples", 0)
results = [
f"CPU Usage Difference: {cpu_diff}",
f"Memory Usage Difference: {memory_diff} bytes"
]
with open("profiling_diff.txt", "w") as f:
f.write("\\n".join(results) + "\\n")
print("\\n".join(results)) # Print results to terminal
except Exception as e:
error_message = f"Error comparing profiling results: {e}"
with open("profiling_diff.txt", "w") as f:
f.write(error_message + "\\n")
print(error_message) # Print error to terminal
'

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🛠️ Refactor suggestion

Move Python comparison logic to a separate script

The embedded Python script should be moved to a separate file for better maintainability and testing.

Create a new file scripts/compare_profiles.py:

import json
import sys
from typing import Dict, Any

def compare_profiles(base_file: str, head_file: str) -> Dict[str, Any]:
    try:
        with open(base_file) as f:
            base = json.load(f)
        with open(head_file) as f:
            head = json.load(f)
            
        return {
            'cpu_diff': head.get('total_cpu_samples_python', 0) - base.get('total_cpu_samples_python', 0),
            'memory_diff': head.get('malloc_samples', 0) - base.get('malloc_samples', 0)
        }
    except Exception as e:
        return {'error': str(e)}

if __name__ == '__main__':
    results = compare_profiles('base_results.json', 'head_results.json')
    with open('profiling_diff.txt', 'w') as f:
        if 'error' in results:
            f.write(f"Error comparing profiling results: {results['error']}\n")
        else:
            f.write(f"CPU Usage Difference: {results['cpu_diff']}\n")
            f.write(f"Memory Usage Difference: {results['memory_diff']} bytes\n")

Then update the workflow:

 - name: Compare profiling results
   run: |
-    python -c '...'
+    python scripts/compare_profiles.py

- name: Upload profiling diff artifact
uses: actions/upload-artifact@v3
with:
name: profiling-diff
path: profiling_diff.txt

# Post results to the pull request
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@borisarzentar borisarzentar Dec 6, 2024

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We can upload this diff result as artifact -> https://github.com/actions/upload-artifact

# - name: Post profiling results to PR
# uses: actions/github-script@v6
# with:
# script: |
# const fs = require('fs');
# const diff = fs.readFileSync('profiling_diff.txt', 'utf-8');
# github.rest.issues.createComment({
# issue_number: context.issue.number,
# owner: context.repo.owner,
# repo: context.repo.repo,
# body: `### Profiling Results for code_graph_pipeline.py\n\`\`\`\n${diff || 'No differences found.'}\n\`\`\``
# });
Comment on lines +125 to +137
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🛠️ Refactor suggestion

Enable PR comment creation for visibility

The PR comment creation is currently commented out. This should be enabled to make profiling results visible to reviewers.

-#    - name: Post profiling results to PR
-#      uses: actions/github-script@v6
+    - name: Post profiling results to PR
+      if: github.event_name == 'pull_request'
+      uses: actions/github-script@v7
+      with:
+        script: |
+          const fs = require('fs');
+          const diff = fs.readFileSync('profiling_diff.txt', 'utf-8');
+          const body = `### Profiling Results for code_graph_pipeline.py
+          
+          \`\`\`
+          ${diff || 'No differences found.'}
+          \`\`\`
+          
+          <details>
+          <summary>About this profiling</summary>
+          
+          - Base SHA: \`${{ env.BASE_SHA }}\`
+          - Head SHA: \`${{ env.HEAD_SHA }}\`
+          - Tool: pyinstrument
+          </details>`;
+          
+          await github.rest.issues.createComment({
+            issue_number: context.issue.number,
+            owner: context.repo.owner,
+            repo: context.repo.repo,
+            body
+          });
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
# Post results to the pull request
# - name: Post profiling results to PR
# uses: actions/github-script@v6
# with:
# script: |
# const fs = require('fs');
# const diff = fs.readFileSync('profiling_diff.txt', 'utf-8');
# github.rest.issues.createComment({
# issue_number: context.issue.number,
# owner: context.repo.owner,
# repo: context.repo.repo,
# body: `### Profiling Results for code_graph_pipeline.py\n\`\`\`\n${diff || 'No differences found.'}\n\`\`\``
# });
- name: Post profiling results to PR
if: github.event_name == 'pull_request'
uses: actions/github-script@v7
with:
script: |
const fs = require('fs');
const diff = fs.readFileSync('profiling_diff.txt', 'utf-8');
const body = `### Profiling Results for code_graph_pipeline.py
\`\`\`
${diff || 'No differences found.'}
\`\`\`
<details>
<summary>About this profiling</summary>
- Base SHA: \`${{ env.BASE_SHA }}\`
- Head SHA: \`${{ env.HEAD_SHA }}\`
- Tool: pyinstrument
</details>`;
await github.rest.issues.createComment({
issue_number: context.issue.number,
owner: context.repo.owner,
repo: context.repo.repo,
body
});

6 changes: 0 additions & 6 deletions .github/workflows/py_lint.yml
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Expand Up @@ -13,14 +13,8 @@ concurrency:
cancel-in-progress: true

jobs:
get_docs_changes:
name: docs changes
uses: ./.github/workflows/get_docs_changes.yml

run_lint:
name: lint
needs: get_docs_changes
if: needs.get_docs_changes.outputs.changes_outside_docs == 'true'
strategy:
fail-fast: true
matrix:
Expand Down
5 changes: 0 additions & 5 deletions .github/workflows/reusable_notebook.yml
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Expand Up @@ -19,14 +19,9 @@ env:
RUNTIME__LOG_LEVEL: ERROR

jobs:
get_docs_changes:
name: docs changes
uses: ./.github/workflows/get_docs_changes.yml

run_notebook_test:
name: test
needs: get_docs_changes
if: needs.get_docs_changes.outputs.changes_outside_docs == 'true' && ${{ github.event.label.name == 'run-checks' }}
runs-on: ubuntu-latest
defaults:
run:
Expand Down
5 changes: 0 additions & 5 deletions .github/workflows/reusable_python_example.yml
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Expand Up @@ -19,14 +19,9 @@ env:
RUNTIME__LOG_LEVEL: ERROR

jobs:
get_docs_changes:
name: docs changes
uses: ./.github/workflows/get_docs_changes.yml

run_notebook_test:
name: test
needs: get_docs_changes
if: needs.get_docs_changes.outputs.changes_outside_docs == 'true' && ${{ github.event.label.name == 'run-checks' }}
runs-on: ubuntu-latest
defaults:
run:
Expand Down
5 changes: 0 additions & 5 deletions .github/workflows/test_milvus.yml
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Expand Up @@ -14,14 +14,9 @@ env:
ENV: 'dev'

jobs:
get_docs_changes:
name: docs changes
uses: ./.github/workflows/get_docs_changes.yml

run_milvus:
name: test
needs: get_docs_changes
if: needs.get_docs_changes.outputs.changes_outside_docs == 'true' && ${{ github.event.label.name == 'run-checks' }}
runs-on: ubuntu-latest
strategy:
fail-fast: false
Expand Down
6 changes: 0 additions & 6 deletions .github/workflows/test_neo4j.yml
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Expand Up @@ -13,14 +13,8 @@ env:
RUNTIME__LOG_LEVEL: ERROR

jobs:
get_docs_changes:
name: docs changes
uses: ./.github/workflows/get_docs_changes.yml

run_neo4j_integration_test:
name: test
needs: get_docs_changes
if: needs.get_docs_changes.outputs.changes_outside_docs == 'true' && ${{ github.event.label.name == 'run-checks' }}
runs-on: ubuntu-latest

defaults:
Expand Down
5 changes: 0 additions & 5 deletions .github/workflows/test_pgvector.yml
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Expand Up @@ -14,14 +14,9 @@ env:
RUNTIME__LOG_LEVEL: ERROR

jobs:
get_docs_changes:
name: docs changes
uses: ./.github/workflows/get_docs_changes.yml

run_pgvector_integration_test:
name: test
needs: get_docs_changes
if: needs.get_docs_changes.outputs.changes_outside_docs == 'true' && ${{ github.event.label.name == 'run-checks' }}
runs-on: ubuntu-latest
defaults:
run:
Expand Down
5 changes: 0 additions & 5 deletions .github/workflows/test_python_3_10.yml
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Expand Up @@ -14,14 +14,9 @@ env:
ENV: 'dev'

jobs:
get_docs_changes:
name: docs changes
uses: ./.github/workflows/get_docs_changes.yml

run_common:
name: test
needs: get_docs_changes
if: needs.get_docs_changes.outputs.changes_outside_docs == 'true' && ${{ github.event.label.name == 'run-checks' }}
runs-on: ubuntu-latest
strategy:
fail-fast: false
Expand Down
5 changes: 0 additions & 5 deletions .github/workflows/test_python_3_11.yml
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Expand Up @@ -14,14 +14,9 @@ env:
ENV: 'dev'

jobs:
get_docs_changes:
name: docs changes
uses: ./.github/workflows/get_docs_changes.yml

run_common:
name: test
needs: get_docs_changes
if: needs.get_docs_changes.outputs.changes_outside_docs == 'true' && ${{ github.event.label.name == 'run-checks' }}
runs-on: ubuntu-latest
strategy:
fail-fast: false
Expand Down
5 changes: 0 additions & 5 deletions .github/workflows/test_python_3_9.yml
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Expand Up @@ -14,14 +14,9 @@ env:
ENV: 'dev'

jobs:
get_docs_changes:
name: docs changes
uses: ./.github/workflows/get_docs_changes.yml

run_common:
name: test
needs: get_docs_changes
if: needs.get_docs_changes.outputs.changes_outside_docs == 'true' && ${{ github.event.label.name == 'run-checks' }}
runs-on: ubuntu-latest
strategy:
fail-fast: false
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5 changes: 0 additions & 5 deletions .github/workflows/test_qdrant.yml
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Expand Up @@ -14,14 +14,9 @@ env:
RUNTIME__LOG_LEVEL: ERROR

jobs:
get_docs_changes:
name: docs changes
uses: ./.github/workflows/get_docs_changes.yml

run_qdrant_integration_test:
name: test
needs: get_docs_changes
if: needs.get_docs_changes.outputs.changes_outside_docs == 'true' && ${{ github.event.label.name == 'run-checks' }}
runs-on: ubuntu-latest

defaults:
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5 changes: 0 additions & 5 deletions .github/workflows/test_weaviate.yml
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Expand Up @@ -14,14 +14,9 @@ env:
RUNTIME__LOG_LEVEL: ERROR

jobs:
get_docs_changes:
name: docs changes
uses: ./.github/workflows/get_docs_changes.yml

run_weaviate_integration_test:
name: test
needs: get_docs_changes
if: needs.get_docs_changes.outputs.changes_outside_docs == 'true' && ${{ github.event.label.name == 'run-checks' }}
runs-on: ubuntu-latest

defaults:
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