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Fix alembic.ini and alembic/ not included in wheel distribution #4180

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opened 2026-04-06 18:14:59 +00:00 by CoreRasurae · 3 comments
CoreRasurae commented 2026-04-06 18:14:59 +00:00
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Metadata

  • Commit Message: fix(database): include alembic files in package distribution
  • Branch: fix/alembic-distribution

Background and Context

When running agents init inside a Docker container built from the current Dockerfile, the application fails with:

FileNotFoundError: Alembic configuration file (alembic.ini) not found. 
Searched upward from: /usr/local/lib/python3.13/site-packages/cleveragents

The root cause is that alembic files (alembic.ini and the alembic/ directory) are located at the repository root but are not included in the Python wheel distribution. When the wheel is built and installed, Python packaging only includes files from the declared packages directory (src/cleveragents) and explicitly listed include files in pyproject.toml. Since the alembic files don't meet either criterion, they are silently omitted.

Affected code:

  • MigrationRunner._find_alembic_ini() in src/cleveragents/infrastructure/database/migration_runner.py:35-89 — searches for alembic.ini by walking upward from the package root, assuming it's in a predictable location relative to the installed package
  • Dockerfile (lines 16-17) — only copies src/ directory, not the repository-root alembic/ directory and alembic.ini
  • pyproject.toml (lines 109-111) — wheel build configuration only includes src/cleveragents package

This is a critical blocker for containerized deployments and any installation method that relies on the wheel distribution.

Current Behavior

  1. Docker image is built with python -m build --wheel
  2. Wheel is installed with pip install /tmp/*.whl
  3. When agents init is executed, it calls MigrationRunner.init_or_upgrade()
  4. init_or_upgrade() triggers alembic_cfg property, which calls _find_alembic_ini()
  5. _find_alembic_ini() searches for alembic.ini by walking up 10 levels from src/cleveragents or infrastructure/database
  6. The file is not found because it's not part of the installed wheel
  7. FileNotFoundError is raised and wrapped as INTERNAL [500] error

Expected Behavior

When running agents init in any deployment mode (Docker, local install, editable install), the application should:

  1. Successfully locate alembic.ini and the migration scripts
  2. Apply any pending database migrations without errors
  3. Initialize the database schema correctly

Acceptance Criteria

  1. Alembic files are properly packaged — alembic.ini and the alembic/ directory (with all migration scripts) are included in the built wheel
  2. MigrationRunner works in all deployment contexts — agents init succeeds in:
    • Docker containers (wheel-based install)
    • Local pip install (wheel or editable)
    • Development environments (editable install with pip install -e .)
  3. No modification to alembic search logic — the current search strategy in _find_alembic_ini() remains unchanged; we're only ensuring files are present
  4. Migration tests pass — existing migration-related tests in the test suite continue to pass with the new structure

Supporting Information

  • Configuration issue: pyproject.toml lines 109-111 define the wheel build configuration but do not include alembic files
  • Docker issue: Dockerfile lines 16-17 only copy source files, not repository-root assets
  • Test the fix: Run docker build -t cleveragents . && docker run cleveragents agents init test-project — this should succeed without errors

Solution Options

The project owner and maintainers must choose between Option 1 (Recommended) and Option 2 below. Both solve the problem; they represent different philosophical approaches to package organization.

Option 1: Move alembic files into the package ⭐ RECOMMENDED

Approach: Reorganize alembic files into the standard Python package structure.

Changes:

  1. Move alembic/ directory from repository root to src/cleveragents/infrastructure/database/migrations/
  2. Move alembic.ini to src/cleveragents/infrastructure/database/migrations/alembic.ini
  3. Update alembic.ini — change script_location from %(here)s/alembic to %(here)s/versions (the migrations directory)
  4. Update MigrationRunner._find_alembic_ini() to search from src/cleveragents/infrastructure/database/migrations/ as the primary anchor point
  5. No changes required to pyproject.toml (files in src/cleveragents/ are automatically included)
  6. Update Dockerfile — no changes needed; alembic files are now part of the package

Advantages:

  • ✅ Standard Python packaging practice — alembic files are part of the package code
  • ✅ Works in all deployment modes without special configuration (wheel, editable, local install)
  • ✅ No changes to pyproject.toml required
  • ✅ No Docker special cases required
  • ✅ Portable and maintainable long-term
  • ✅ If the package is published to PyPI, alembic files are automatically included

Disadvantages:

  • ⚠️ Reorganizes directory structure (may require refactoring of any other code that references alembic paths)
  • ⚠️ Alembic files are now "buried" in src/cleveragents/infrastructure/database/migrations/ rather than at repo root (but this is standard practice)

Subtasks

  • Implement chosen solution:
    • Move alembic/ directory to src/cleveragents/infrastructure/database/migrations/
    • Move alembic.ini to src/cleveragents/infrastructure/database/migrations/alembic.ini
    • Update alembic.ini script_location setting to correct relative path
    • Update MigrationRunner._find_alembic_ini() to search from new location
    • Update any documentation that references alembic file locations
  • Tests (Behave): Add scenarios for database initialization in containerized/packaged contexts
  • Tests (Robot): Add integration test for agents init in a fresh environment
  • Manual testing: Build Docker image and verify agents init <project> succeeds
  • Verify coverage ≥97% via nox -s coverage_report
  • Run full test suite: nox (all default sessions), fix any errors
  • Update documentation: Update any relevant docs that mention alembic file organization or installation

Definition of Done

This issue is complete when:

  • All subtasks above are completed and checked off
  • A Git commit is created where the first line of the commit message matches the Commit Message in Metadata exactly, followed by a blank line, then additional lines describing the implementation
  • The commit is pushed to the remote on the branch matching the Branch in Metadata exactly
  • The commit is submitted as a pull request to master, reviewed, and merged before this issue is marked done
  • agents init successfully runs in a Docker container built from the updated Dockerfile without FileNotFoundError
  • All tests pass, including migration-specific tests
  • Test coverage remains ≥97%
## Metadata - **Commit Message**: `fix(database): include alembic files in package distribution` - **Branch**: `fix/alembic-distribution` ## Background and Context When running `agents init` inside a Docker container built from the current Dockerfile, the application fails with: ``` FileNotFoundError: Alembic configuration file (alembic.ini) not found. Searched upward from: /usr/local/lib/python3.13/site-packages/cleveragents ``` The root cause is that alembic files (`alembic.ini` and the `alembic/` directory) are located at the repository root but are **not included** in the Python wheel distribution. When the wheel is built and installed, Python packaging only includes files from the declared `packages` directory (`src/cleveragents`) and explicitly listed `include` files in `pyproject.toml`. Since the alembic files don't meet either criterion, they are silently omitted. **Affected code:** - `MigrationRunner._find_alembic_ini()` in `src/cleveragents/infrastructure/database/migration_runner.py:35-89` — searches for `alembic.ini` by walking upward from the package root, assuming it's in a predictable location relative to the installed package - Dockerfile (lines 16-17) — only copies `src/` directory, not the repository-root `alembic/` directory and `alembic.ini` - `pyproject.toml` (lines 109-111) — wheel build configuration only includes `src/cleveragents` package This is a critical blocker for containerized deployments and any installation method that relies on the wheel distribution. ## Current Behavior 1. Docker image is built with `python -m build --wheel` 2. Wheel is installed with `pip install /tmp/*.whl` 3. When `agents init` is executed, it calls `MigrationRunner.init_or_upgrade()` 4. `init_or_upgrade()` triggers `alembic_cfg` property, which calls `_find_alembic_ini()` 5. `_find_alembic_ini()` searches for `alembic.ini` by walking up 10 levels from `src/cleveragents` or `infrastructure/database` 6. The file is not found because it's not part of the installed wheel 7. `FileNotFoundError` is raised and wrapped as `INTERNAL [500]` error ## Expected Behavior When running `agents init` in any deployment mode (Docker, local install, editable install), the application should: 1. Successfully locate `alembic.ini` and the migration scripts 2. Apply any pending database migrations without errors 3. Initialize the database schema correctly ## Acceptance Criteria 1. **Alembic files are properly packaged** — `alembic.ini` and the `alembic/` directory (with all migration scripts) are included in the built wheel 2. **MigrationRunner works in all deployment contexts** — `agents init` succeeds in: - Docker containers (wheel-based install) - Local pip install (wheel or editable) - Development environments (editable install with `pip install -e .`) 3. **No modification to alembic search logic** — the current search strategy in `_find_alembic_ini()` remains unchanged; we're only ensuring files are present 4. **Migration tests pass** — existing migration-related tests in the test suite continue to pass with the new structure ## Supporting Information - **Configuration issue**: `pyproject.toml` lines 109-111 define the wheel build configuration but do not include alembic files - **Docker issue**: `Dockerfile` lines 16-17 only copy source files, not repository-root assets - **Test the fix**: Run `docker build -t cleveragents . && docker run cleveragents agents init test-project` — this should succeed without errors --- ## Solution Options The project owner and maintainers must choose between **Option 1** (Recommended) and **Option 2** below. Both solve the problem; they represent different philosophical approaches to package organization. ### Option 1: Move alembic files into the package ⭐ **RECOMMENDED** **Approach:** Reorganize alembic files into the standard Python package structure. **Changes:** 1. Move `alembic/` directory from repository root to `src/cleveragents/infrastructure/database/migrations/` 2. Move `alembic.ini` to `src/cleveragents/infrastructure/database/migrations/alembic.ini` 3. Update `alembic.ini` — change `script_location` from `%(here)s/alembic` to `%(here)s/versions` (the migrations directory) 4. Update `MigrationRunner._find_alembic_ini()` to search from `src/cleveragents/infrastructure/database/migrations/` as the primary anchor point 5. No changes required to `pyproject.toml` (files in `src/cleveragents/` are automatically included) 6. Update `Dockerfile` — no changes needed; alembic files are now part of the package **Advantages:** - ✅ Standard Python packaging practice — alembic files are part of the package code - ✅ Works in all deployment modes without special configuration (wheel, editable, local install) - ✅ No changes to `pyproject.toml` required - ✅ No Docker special cases required - ✅ Portable and maintainable long-term - ✅ If the package is published to PyPI, alembic files are automatically included **Disadvantages:** - ⚠️ Reorganizes directory structure (may require refactoring of any other code that references alembic paths) - ⚠️ Alembic files are now "buried" in `src/cleveragents/infrastructure/database/migrations/` rather than at repo root (but this is standard practice) --- ## Subtasks - [ ] **Implement chosen solution**: - [ ] Move `alembic/` directory to `src/cleveragents/infrastructure/database/migrations/` - [ ] Move `alembic.ini` to `src/cleveragents/infrastructure/database/migrations/alembic.ini` - [ ] Update `alembic.ini` `script_location` setting to correct relative path - [ ] Update `MigrationRunner._find_alembic_ini()` to search from new location - [ ] Update any documentation that references alembic file locations - [ ] **Tests (Behave)**: Add scenarios for database initialization in containerized/packaged contexts - [ ] **Tests (Robot)**: Add integration test for `agents init` in a fresh environment - [ ] **Manual testing**: Build Docker image and verify `agents init <project>` succeeds - [ ] **Verify coverage** ≥97% via `nox -s coverage_report` - [ ] **Run full test suite**: `nox` (all default sessions), fix any errors - [ ] **Update documentation**: Update any relevant docs that mention alembic file organization or installation ## Definition of Done This issue is complete when: - All subtasks above are completed and checked off - A Git commit is created where the **first line** of the commit message matches the Commit Message in Metadata exactly, followed by a blank line, then additional lines describing the implementation - The commit is pushed to the remote on the branch matching the **Branch** in Metadata exactly - The commit is submitted as a **pull request** to `master`, reviewed, and **merged** before this issue is marked done - `agents init` successfully runs in a Docker container built from the updated Dockerfile without `FileNotFoundError` - All tests pass, including migration-specific tests - Test coverage remains ≥97%
CoreRasurae commented 2026-04-06 18:18:58 +00:00
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I believe the best solution is to for Option 1 since:
Option 1 does NOT violate either CONTRIBUTING.md nor docs/specification.md — in fact, it aligns better with CONTRIBUTING.md's philosophy because:

  1. It moves a non-standard file from the root into an appropriate subdirectory
  2. It co-locates database migrations with other database code (infrastructure/database)
  3. It follows Python packaging best practices (migrations are part of the package)

Please advise.

I believe the best solution is to for Option 1 since: Option 1 does NOT violate either CONTRIBUTING.md nor docs/specification.md — in fact, it aligns better with CONTRIBUTING.md's philosophy because: 1. It moves a non-standard file from the root into an appropriate subdirectory 2. It co-locates database migrations with other database code (infrastructure/database) 3. It follows Python packaging best practices (migrations are part of the package) Please advise.
HAL9000 self-assigned this 2026-04-08 18:49:12 +00:00
HAL9000 added this to the v3.2.0 milestone 2026-04-08 18:49:12 +00:00
HAL9000 commented 2026-04-08 18:49:48 +00:00
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Issue assigned to @HAL9000 and milestone set to v3.2.0.

Milestone Rationale: This is a fundamental build/distribution issue — alembic files are missing from the wheel, which causes agents init to fail in Docker containers. This blocks basic deployment and is core infrastructure that belongs in the earliest milestone.

Assignment Rationale: Default assignment to HAL9000 to maintain velocity. This is a build configuration fix.

Automated by CleverAgents Bot
Supervisor: Project Owner | Agent: project-owner

Issue assigned to @HAL9000 and milestone set to **v3.2.0**. **Milestone Rationale**: This is a fundamental build/distribution issue — alembic files are missing from the wheel, which causes `agents init` to fail in Docker containers. This blocks basic deployment and is core infrastructure that belongs in the earliest milestone. **Assignment Rationale**: Default assignment to HAL9000 to maintain velocity. This is a build configuration fix. --- **Automated by CleverAgents Bot** Supervisor: Project Owner | Agent: project-owner
CoreRasurae commented 2026-04-14 17:09:06 +00:00
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Implementation In Progress

This issue is being addressed by PR #9408: fix(database): include alembic files in package distribution

PR Blocks This Issue - Once merged, this PR will resolve issue #4180 by:

  • Moving alembic configuration and migration files into the Python package structure
  • Ensuring alembic files are included in wheel distributions
  • Allowing agents init to work correctly in Docker containers and other wheel-based installations

Please review the PR for implementation details.

## Implementation In Progress This issue is being addressed by **PR #9408**: [fix(database): include alembic files in package distribution](https://git.cleverthis.com/cleveragents/cleveragents-core/pulls/9408) **PR Blocks This Issue** - Once merged, this PR will resolve issue #4180 by: - Moving alembic configuration and migration files into the Python package structure - Ensuring alembic files are included in wheel distributions - Allowing `agents init` to work correctly in Docker containers and other wheel-based installations Please review the PR for implementation details.
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Detected master commit violating the strict merge invariant. Tracked as an issue (not a PR label); kept here for label completeness.

  
auto/last-attempt-tier-0
In-cycle escalation: most recent attempt ran at the Tier 0 slot (`tier-0`). Slot's model defined in .opencode/models/tiers.yaml.

  
auto/last-attempt-tier-1
In-cycle escalation: most recent attempt ran at the Tier 1 slot (`tier-1`). Slot's model defined in .opencode/models/tiers.yaml.

  
auto/last-attempt-tier-2
In-cycle escalation: most recent attempt ran at the Tier 2 slot (`tier-2`). Slot's model defined in .opencode/models/tiers.yaml. Gated behind IMPLEMENTER_ESCALATION_TIER2_ENABLED.

  
auto/last-attempt-tier-min
In-cycle escalation: most recent attempt ran at the Tier -1 slot (`tier-min`). Slot's model defined in .opencode/models/tiers.yaml. Suffix is ``-min`` (not ``--1``) so the Forgejo UI reads naturally.

  
Automation Tracking
Tracking issues used by the AI Automation system for agents to communicate and report.

  
auto/needs-conflict-resolution
Rebase conflict needs LLM conflict-resolver.

  
auto/needs-implementer
Failing CI needs implementer attention.

  
auto/postmortem
Documenting a driver incident or rollback.

  
auto/ready-to-merge
Reviewer has APPROVED this PR and no later REQUEST_CHANGES is outstanding. The merge driver requires this label to even consider a PR for merging. Set by the reviewer worker on APPROVE; cleared on REQUEST_CHANGES.

  
auto/restart-throttled
Train repeatedly lost master-tempo races. Driver excludes via merge_cycle until cooldown elapses; label persists as visible history.

  
auto/revert
Revert PR backing out an invariant violation. Fast-tracked through the merge driver.

  
auto/sentinel
Sentinel PR duplicated from upstream into a personal fork by tools/duplicate_prs_to_fork.py for pipeline testing. Lives only in the fork; the canonical pipeline never sees it.

  
auto/stale-inactivity
No implementer activity for N days. Flagged for human review. Auto-cleared on next push to head branch.

  
auto/unstable
Repeatedly fails on current master (>= 3 ci-fail-on-rebased-sha releases in 12 h). Excluded from driver until human triage.

  
Blocked
A ticket in a blocked state and unable to complete until some other task is completed first.

  
Bounty
$100
 A bounty of $100 for any open-source contributor who provides a MR that solves this issue

  
Bounty
$1000
 A bounty of $1000 for any open-source contributor who provides a MR that solves this issue

  
Bounty
$10000
 A bounty of $10000 for any open-source contributor who provides a MR that solves this issue

  
Bounty
$20
 A bounty of $20 for any open-source contributor who provides a MR that solves this issue

  
Bounty
$2000
 A bounty of $2000 for any open-source contributor who provides a MR that solves this issue

  
Bounty
$250
 A bounty of $250 for any open-source contributor who provides a MR that solves this issue

  
Bounty
$50
 A bounty of $50 for any open-source contributor who provides a MR that solves this issue

  
Bounty
$500
 A bounty of $500 for any open-source contributor who provides a MR that solves this issue

  
Bounty
$5000
 A bounty of $5000 for any open-source contributor who provides a MR that solves this issue

  
Bounty
$750
 A bounty of $750 for any open-source contributor who provides a MR that solves this issue

  
MoSCoW
Could have
 Could have feature in order to satisfy the epic/legendary.

  
MoSCoW
Must have
 Must have feature in order to satisfy the epic/legendary.

  
MoSCoW
Should have
 Should have feature in order to satisfy the epic/legendary.

  
Needs Feedback
There are questions in the ticket that can not be completed until the project owner provides clarity.

  
Points
1
 1 man-hours worth of work for an expert with no learning curve.

  
Points
13
 13 man-hours worth of work for an expert with no learning curve.

  
Points
2
 2 man-hours worth of work for an expert with no learning curve.

  
Points
21
 21 man-hours worth of work for an expert with no learning curve.

  
Points
3
 3 man-hours worth of work for an expert with no learning curve.

  
Points
34
 34 man-hours worth of work for an expert with no learning curve.

  
Points
5
 5 man-hours worth of work for an expert with no learning curve.

  
Points
55
 55 man-hours worth of work for an expert with no learning curve.

  
Points
8
 8 man-hours worth of work for an expert with no learning curve.

  
Points
88
 88 man-hours worth of work for an expert with no learning curve.

  
Priority
Backlog
 This ticket has backlogged priority and is not to be worked on yet

  
Priority
CI Blocker
 Critical priority issue that blocks CI/CD pipeline and prevents PR merges

  
Priority
Critical
 The priority is critical

  
Priority
High
 The priority is high

  
Priority
Low
 The priority is low

  
Priority
Medium
 The priority is medium

  
Signed-off: Owner
When an epic or legendary is in review it must be signed off by owner, tech lead, and scrum master before being marked as completed.

  
Signed-off: Scrum Master
When an epic or legendary is in review it must be signed off by owner, tech lead, and scrum master before being marked as completed.

  
Signed-off: Tech Lead
When an epic or legendary is in review it must be signed off by owner, tech lead, and scrum master before being marked as completed.

  
Spike
A ticket for learning a tool or technology that is needed to be able to do future planning and design.

  
State
Completed
 The ticket has been fully implemented, completed, and merged with the source code. This label should only be applied once a ticket is closed.

  
State
Duplicate
 A ticket that represents the same content as an existing ticket.

  
State
In Progress
 A ticket that is actively being developed.

  
State
In Review
 A ticket that has had some code completed to implement but is waiting to pass peer review and is not yet merged in.

  
State
Paused
 This ticket's work started but wasn't finished. It's on hold (likely in a feature branch) and will be resumed later, either due to a blocker or a delay.

  
State
Unverified
 All new tickets start in this state. A developer may set it to show the ticket is unverified. This means we haven't agreed to work on it. It will either move to a verified state or be closed as wontdo.

  
State
Verified
 The issue has been verified by a developer as legitimate. It will be worked on and verified tickets are now considered part of the backlog.

  
State
Wont Do
 This ticket has been decided it wont be done. This may mean the bug has been determined to not be real (cant verify) or the feature is one we have decided we dont want to adopt.

  
Type
Automation
 Any edits or discussion about the AI automated coding system.

  
Type
Bug
 Something that doesnt work as intended.

  
Type
Discussion
 Anytime a ticket represents a discussion about a subject and doesnt fall into one of the other categories.

  
Type
Documentation
 An error or improvement needed in the documentation.

  
Type
Epic
 Any first tier epic. That is, an epic which contains only issues as children and will not have sub-epics.

  
Type
Feature
 Some new functionality not present.

  
Type
Legendary
 A type of Epic which will contain other Epics.

  
Type
Refactor
 A code change that restructures existing code without changing its external behavior.

  
Type
Support
 Someone needs help using the project.

  
Type
Task
 A generic task that doesnt fit into the other type categories.

  
Type
Testing
 Work exclusively focusing on fixing or expanding testing.

No labels
auto/needs-reevaluation
controller-managed
auto/blocked-by-deps
auto/ci-timeout
auto/claimed-implementer
auto/claimed-merge
auto/claimed-reviewer
auto/driver-down
auto/invariant-violation
auto/last-attempt-tier-0
auto/last-attempt-tier-1
auto/last-attempt-tier-2
auto/last-attempt-tier-min
Automation Tracking
auto/needs-conflict-resolution
auto/needs-implementer
auto/postmortem
auto/ready-to-merge
auto/restart-throttled
auto/revert
auto/sentinel
auto/stale-inactivity
auto/unstable
Blocked
Bounty
$100
Bounty
$1000
Bounty
$10000
Bounty
$20
Bounty
$2000
Bounty
$250
Bounty
$50
Bounty
$500
Bounty
$5000
Bounty
$750
MoSCoW
Could have
MoSCoW
Must have
MoSCoW
Should have
Needs Feedback
Points
1
Points
13
Points
2
Points
21
Points
3
Points
34
Points
5
Points
55
Points
8
Points
88
Priority
Backlog
Priority
CI Blocker
Priority
Critical
Priority
High
Priority
Low
Priority
Medium
Signed-off: Owner
Signed-off: Scrum Master
Signed-off: Tech Lead
Spike
State
Completed
State
Duplicate
State
In Progress
State
In Review
State
Paused
State
Unverified
State
Verified
State
Wont Do
Type
Automation
Type
Bug
Type
Discussion
Type
Documentation
Type
Epic
Type
Feature
Type
Legendary
Type
Refactor
Type
Support
Type
Task
Type
Testing
Milestone
Clear milestone
No items
No milestone
v3.2.0
Projects
Clear projects
No items
No project
Assignees
Clear assignees
No assignees
HAL9000
2 participants
Notifications
Due date
The due date is invalid or out of range. Please use the format "yyyy-mm-dd".

No due date set.

Depends on
#9408 fix(database): include alembic files in package distribution
cleveragents/cleveragents-core
Reference
cleveragents/cleveragents-core#4180
No description provided.