canns 1.0.0__tar.gz → 1.0.1__tar.gz

{canns-1.0.0 → canns-1.0.1}/.gitignore

@@ -186,6 +186,7 @@ cython_debug/
 *.npy
 *.png
 !docs/_static/*.png
+!docs/_static/*.gif
 /.ref
 
 # Model checkpoints

{canns-1.0.0 → canns-1.0.1}/CHANGELOG.md

@@ -5,12 +5,37 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.0.1] - 2026-02-06
+
+### Added
+- CLI module (`src/canns/__main__.py`) for command-line interface support
+- Comprehensive test coverage for CLI, lazy imports, data loaders, and utilities
+- Integration tests for pipeline launcher
+- Unit tests for task base classes and benchmarking utilities
+- 1D CANN smooth-tracking example in documentation
+
+### Changed
+- Restructured test suite into `unit/` and `integration/` directories (PR #96)
+- Optimized CI pipeline for faster test execution (PR #96)
+- Relocated documentation images from `images/` to `docs/_static/`
+- Updated status badge to "stable" and maintenance year to 2026
+- Enhanced installation instructions with accelerator options (cuda12, cuda13, tpu, gui)
+- Expanded architecture diagram caption with five-layer hierarchy description
+- Normalized pip install examples by removing unnecessary quotes
+- Updated documentation URL to https://routhleck.com/canns
+- Added Zenodo DOI badge for v1.0.0 release
+- Updated citation information with expanded author list and affiliations
+
+### Fixed
+- Improved test organization and maintainability
+- Updated all documentation image references to new paths
+
 ## [1.0.0] - 2026-02-02
 
 ### Added
-- Architecture diagram (`images/architecture.png`) explaining modular design principles
-- Comprehensive analyzer visualization showcase (`images/analyzer-display.png`, 4.7MB)
-- ASA GUI preview animation (`images/asa-gui.gif`, 898KB)
+- Architecture diagram (`docs/_static/architecture.png`) explaining modular design principles
+- Comprehensive analyzer visualization showcase (`docs/_static/analyzer-display.png`, 4.7MB)
+- ASA GUI preview animation (`docs/_static/asa-gui.gif`, 898KB)
 
 ### Changed
 - **Production Ready Milestone**: v1.0.0 marks API stability and production readiness
@@ -235,7 +260,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Comprehensive plotting functions for ASA analysis types
 - New example scripts: cohomap.py, cohospace.py, firing_field_map.py, path_compare.py, tda_vis.py
 - Research paper draft (paper.md) with comprehensive bibliography (paper.bib)
-- Architecture diagram (images/architecture.png)
+- Architecture diagram (docs/_static/architecture.png)
 - GitHub Actions workflow for draft PDF generation
 - CLI entry point for ASA TUI: `python -m canns.pipeline.asa`
 - Image preview and external viewer support in TUI
@@ -602,6 +627,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Basic structure template
 - Core application structure
 
+[1.0.1]: https://github.com/routhleck/canns/compare/v1.0.0...v1.0.1
 [1.0.0]: https://github.com/routhleck/canns/compare/v0.15.1...v1.0.0
 [0.15.1]: https://github.com/routhleck/canns/compare/v0.15.0...v0.15.1
 [0.15.0]: https://github.com/routhleck/canns/compare/v0.14.3...v0.15.0
@@ -642,4 +668,4 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 [0.4.0]: https://github.com/routhleck/canns/compare/v0.3.0...v0.4.0
 [0.3.0]: https://github.com/routhleck/canns/compare/v0.2.0...v0.3.0
 [0.2.0]: https://github.com/routhleck/canns/compare/v0.1.0...v0.2.0
-[0.1.0]: https://github.com/routhleck/canns/releases/tag/v0.1.0
+[0.1.0]: https://github.com/routhleck/canns/releases/tag/v0.1.0

canns-1.0.1/CITATION.cff

@@ -0,0 +1,139 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+type: software
+title: "CANNs: Continuous Attractor Neural Networks Toolkit"
+authors:
+  - family-names: "He"
+    given-names: "Sichao"
+    email: "sichaohe@outlook.com"
+    affiliation:
+      - "School of Psychological and Cognitive Sciences, Peking University"
+      - "Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University"
+      - "PKU-IDG/McGovern Institute for Brain Research, Peking University"
+      - "Center of Quantitative Biology, Peking University"
+    orcid: "https://orcid.org/0009-0009-4564-1753"
+  - family-names: "Tuerhong"
+    given-names: "Aiersi"
+    affiliation: "College of Mathematics and Statistics, Chongqing University"
+    orcid: "https://orcid.org/0009-0006-4603-4734"
+  - family-names: "She"
+    given-names: "Shangjun"
+    affiliation:
+      - "School of Psychological and Cognitive Sciences, Peking University"
+      - "Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University"
+      - "PKU-IDG/McGovern Institute for Brain Research, Peking University"
+      - "Center of Quantitative Biology, Peking University"
+    orcid: "https://orcid.org/0009-0008-4490-7612"
+  - family-names: "Chu"
+    given-names: "Tianhao"
+    affiliation:
+      - "School of Psychological and Cognitive Sciences, Peking University"
+      - "Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University"
+      - "PKU-IDG/McGovern Institute for Brain Research, Peking University"
+      - "Center of Quantitative Biology, Peking University"
+    orcid: "https://orcid.org/0000-0001-9910-9361"
+  - family-names: "Wu"
+    given-names: "Yuling"
+    affiliation:
+      - "School of Psychological and Cognitive Sciences, Peking University"
+      - "Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University"
+      - "PKU-IDG/McGovern Institute for Brain Research, Peking University"
+      - "Center of Quantitative Biology, Peking University"
+    orcid: "https://orcid.org/0009-0001-5303-5413"
+  - family-names: "Zuo"
+    given-names: "Junfeng"
+    affiliation:
+      - "School of Psychological and Cognitive Sciences, Peking University"
+      - "Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University"
+      - "PKU-IDG/McGovern Institute for Brain Research, Peking University"
+      - "Center of Quantitative Biology, Peking University"
+  - family-names: "Wu"
+    given-names: "Si"
+    affiliation:
+      - "School of Psychological and Cognitive Sciences, Peking University"
+      - "Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University"
+      - "PKU-IDG/McGovern Institute for Brain Research, Peking University"
+      - "Center of Quantitative Biology, Peking University"
+    orcid: "https://orcid.org/0000-0001-9650-6935"
+repository-code: "https://github.com/Routhleck/canns"
+url: "https://routhleck.com/canns"
+abstract: "A research toolkit built on BrainPy and JAX that bundles model collections, task generators, analyzers, and the ASA pipeline (GUI/TUI) so researchers can run simulations and analyze results in a consistent workflow."
+keywords:
+  - continuous attractor neural networks
+  - CANNs
+  - computational neuroscience
+  - spatial cognition
+  - neural dynamics
+  - JAX
+  - brain-inspired computing
+license: Apache-2.0
+version: "v1.0.0"
+date-released: "2026-02-02"
+identifiers:
+  - type: doi
+    value: "10.5281/zenodo.18453893"
+    description: "The versioned DOI for version v1.0.0"
+  - type: doi
+    value: "10.5281/zenodo.17412545"
+    description: "The concept DOI (always resolves to latest version)"
+preferred-citation:
+  type: software
+  title: "CANNs: Continuous Attractor Neural Networks Toolkit"
+  authors:
+    - family-names: "He"
+      given-names: "Sichao"
+      email: "sichaohe@outlook.com"
+      affiliation:
+        - "School of Psychological and Cognitive Sciences, Peking University"
+        - "Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University"
+        - "PKU-IDG/McGovern Institute for Brain Research, Peking University"
+        - "Center of Quantitative Biology, Peking University"
+      orcid: "https://orcid.org/0009-0009-4564-1753"
+    - family-names: "Tuerhong"
+      given-names: "Aiersi"
+      affiliation: "College of Mathematics and Statistics, Chongqing University"
+      orcid: "https://orcid.org/0009-0006-4603-4734"
+    - family-names: "She"
+      given-names: "Shangjun"
+      affiliation:
+        - "School of Psychological and Cognitive Sciences, Peking University"
+        - "Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University"
+        - "PKU-IDG/McGovern Institute for Brain Research, Peking University"
+        - "Center of Quantitative Biology, Peking University"
+      orcid: "https://orcid.org/0009-0008-4490-7612"
+    - family-names: "Chu"
+      given-names: "Tianhao"
+      affiliation:
+        - "School of Psychological and Cognitive Sciences, Peking University"
+        - "Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University"
+        - "PKU-IDG/McGovern Institute for Brain Research, Peking University"
+        - "Center of Quantitative Biology, Peking University"
+      orcid: "https://orcid.org/0000-0001-9910-9361"
+    - family-names: "Wu"
+      given-names: "Yuling"
+      affiliation:
+        - "School of Psychological and Cognitive Sciences, Peking University"
+        - "Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University"
+        - "PKU-IDG/McGovern Institute for Brain Research, Peking University"
+        - "Center of Quantitative Biology, Peking University"
+      orcid: "https://orcid.org/0009-0001-5303-5413"
+    - family-names: "Zuo"
+      given-names: "Junfeng"
+      affiliation:
+        - "School of Psychological and Cognitive Sciences, Peking University"
+        - "Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University"
+        - "PKU-IDG/McGovern Institute for Brain Research, Peking University"
+        - "Center of Quantitative Biology, Peking University"
+    - family-names: "Wu"
+      given-names: "Si"
+      affiliation:
+        - "School of Psychological and Cognitive Sciences, Peking University"
+        - "Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University"
+        - "PKU-IDG/McGovern Institute for Brain Research, Peking University"
+        - "Center of Quantitative Biology, Peking University"
+      orcid: "https://orcid.org/0000-0001-9650-6935"
+  doi: "10.5281/zenodo.18453893"
+  url: "https://github.com/Routhleck/canns"
+  version: "v1.0.0"
+  year: 2026
+  month: 2

{canns-1.0.0 → canns-1.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: canns
-Version: 1.0.0
+Version: 1.0.1
 Summary: A Python Library for Continuous Attractor Neural Networks
 Project-URL: Repository, https://github.com/routhleck/canns
 Author-email: Sichao He <sichaohe@outlook.com>
@@ -60,7 +60,7 @@ Description-Content-Type: text/markdown
 [<img src="https://badges.ws/maintenance/yes/2026" />](https://github.com/routhleck/canns)
 <picture><img src="https://badges.ws/github/release/routhleck/canns" /></picture>
 <picture><img src="https://badges.ws/github/license/routhleck/canns" /></picture>
-[![DOI](https://zenodo.org/badge/1001781809.svg)](https://doi.org/10.5281/zenodo.17412545)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18453893.svg)](https://doi.org/10.5281/zenodo.18453893)
 
 
 <picture><img src="https://badges.ws/github/stars/routhleck/canns?logo=github" /></picture>
@@ -77,9 +77,9 @@ CANNs (Continuous Attractor Neural Networks toolkit) is a research toolkit built
 ## Architecture
 
 <p align="center">
-  <img src="images/architecture.png" alt="CANNs Architecture" width="900">
+  <img src="docs/_static/architecture.png" alt="CANNs Architecture" width="900">
   <br>
-  <span style="color: grey; font-size: 14px;">Library architecture overview: models, tasks, analyzers, trainers, and pipeline built on BrainPy/JAX with optional Rust acceleration.</span>
+  <span style="color: grey; font-size: 14px;">Layer hierarchy of the CANNs library showing five levels: Application (Pipeline orchestration), Functional (Task, Trainer, Analyzer, Utils modules), Core Models (CANN implementations), Foundation (BrainPy/JAX and Rust FFI backends), and Hardware (CPU/GPU/TPU support)</span>
 </p>
 
 The CANNs library follows a modular architecture guided by two core principles: **separation of concerns** and **extensibility through
@@ -115,12 +115,12 @@ seamlessly integrate with the built-in ecosystem.
 </p>
 
 <p align="center">
-  <img src="images/analyzer-display.png" alt="Analyzer Display" width="900">
+  <img src="docs/_static/analyzer-display.png" alt="Analyzer Display" width="900">
   <br>
   <span style="color: grey; font-size: 14px;">Rich Analyzer Visualization Results</span>
 </p>
 <p align="center">
-  <img src="images/asa-gui.gif" alt="ASA GUI Preview" width="720">
+  <img src="docs/_static/asa-gui.gif" alt="ASA GUI Preview" width="720">
   <br>
   <span style="color: grey; font-size: 14px;">ASA GUI preview</span>
 </p>
@@ -229,12 +229,12 @@ energy_landscape_1d_animation(
 pip install canns
 
 # Optional accelerators (Linux)
-pip install "canns[cuda12]"
-pip install "canns[cuda13]"
-pip install "canns[tpu]"
+pip install canns[cuda12]
+pip install canns[cuda13]
+pip install canns[tpu]
 
 # GUI (ASA Pipeline)
-pip install "canns[gui]"
+pip install canns[gui]
 ```
 
 Optional (uv):
@@ -250,6 +250,32 @@ uv pip install canns
 - Sphinx docs and notebooks: `docs/`
 - ASA GUI entry: `canns-gui`
 
+## Citation
+
+If you use CANNs in your research, please cite:
+
+```bibtex
+@software{he_2026_canns,
+  author       = {He, Sichao and
+                  Tuerhong, Aiersi and
+                  She, Shangjun and
+                  Chu, Tianhao and
+                  Wu, Yuling and
+                  Zuo, Junfeng and
+                  Wu, Si},
+  title        = {CANNs: Continuous Attractor Neural Networks Toolkit},
+  month        = feb,
+  year         = 2026,
+  publisher    = {Zenodo},
+  version      = {v1.0.0},
+  doi          = {10.5281/zenodo.18453893},
+  url          = {https://doi.org/10.5281/zenodo.18453893}
+}
+```
+
+**Plain text:**
+> He, S., Tuerhong, A., She, S., Chu, T., Wu, Y., Zuo, J., & Wu, S. (2026). CANNs: Continuous Attractor Neural Networks Toolkit (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.18453893
+
 ## Contributing & License
 
 Contributions are welcome. Please read [CONTRIBUTING.md](CONTRIBUTING.md) before opening a PR.

{canns-1.0.0 → canns-1.0.1}/README.md

@@ -9,7 +9,7 @@
 [<img src="https://badges.ws/maintenance/yes/2026" />](https://github.com/routhleck/canns)
 <picture><img src="https://badges.ws/github/release/routhleck/canns" /></picture>
 <picture><img src="https://badges.ws/github/license/routhleck/canns" /></picture>
-[![DOI](https://zenodo.org/badge/1001781809.svg)](https://doi.org/10.5281/zenodo.17412545)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18453893.svg)](https://doi.org/10.5281/zenodo.18453893)
 
 
 <picture><img src="https://badges.ws/github/stars/routhleck/canns?logo=github" /></picture>
@@ -26,9 +26,9 @@ CANNs (Continuous Attractor Neural Networks toolkit) is a research toolkit built
 ## Architecture
 
 <p align="center">
-  <img src="images/architecture.png" alt="CANNs Architecture" width="900">
+  <img src="docs/_static/architecture.png" alt="CANNs Architecture" width="900">
   <br>
-  <span style="color: grey; font-size: 14px;">Library architecture overview: models, tasks, analyzers, trainers, and pipeline built on BrainPy/JAX with optional Rust acceleration.</span>
+  <span style="color: grey; font-size: 14px;">Layer hierarchy of the CANNs library showing five levels: Application (Pipeline orchestration), Functional (Task, Trainer, Analyzer, Utils modules), Core Models (CANN implementations), Foundation (BrainPy/JAX and Rust FFI backends), and Hardware (CPU/GPU/TPU support)</span>
 </p>
 
 The CANNs library follows a modular architecture guided by two core principles: **separation of concerns** and **extensibility through
@@ -64,12 +64,12 @@ seamlessly integrate with the built-in ecosystem.
 </p>
 
 <p align="center">
-  <img src="images/analyzer-display.png" alt="Analyzer Display" width="900">
+  <img src="docs/_static/analyzer-display.png" alt="Analyzer Display" width="900">
   <br>
   <span style="color: grey; font-size: 14px;">Rich Analyzer Visualization Results</span>
 </p>
 <p align="center">
-  <img src="images/asa-gui.gif" alt="ASA GUI Preview" width="720">
+  <img src="docs/_static/asa-gui.gif" alt="ASA GUI Preview" width="720">
   <br>
   <span style="color: grey; font-size: 14px;">ASA GUI preview</span>
 </p>
@@ -178,12 +178,12 @@ energy_landscape_1d_animation(
 pip install canns
 
 # Optional accelerators (Linux)
-pip install "canns[cuda12]"
-pip install "canns[cuda13]"
-pip install "canns[tpu]"
+pip install canns[cuda12]
+pip install canns[cuda13]
+pip install canns[tpu]
 
 # GUI (ASA Pipeline)
-pip install "canns[gui]"
+pip install canns[gui]
 ```
 
 Optional (uv):
@@ -199,6 +199,32 @@ uv pip install canns
 - Sphinx docs and notebooks: `docs/`
 - ASA GUI entry: `canns-gui`
 
+## Citation
+
+If you use CANNs in your research, please cite:
+
+```bibtex
+@software{he_2026_canns,
+  author       = {He, Sichao and
+                  Tuerhong, Aiersi and
+                  She, Shangjun and
+                  Chu, Tianhao and
+                  Wu, Yuling and
+                  Zuo, Junfeng and
+                  Wu, Si},
+  title        = {CANNs: Continuous Attractor Neural Networks Toolkit},
+  month        = feb,
+  year         = 2026,
+  publisher    = {Zenodo},
+  version      = {v1.0.0},
+  doi          = {10.5281/zenodo.18453893},
+  url          = {https://doi.org/10.5281/zenodo.18453893}
+}
+```
+
+**Plain text:**
+> He, S., Tuerhong, A., She, S., Chu, T., Wu, Y., Zuo, J., & Wu, S. (2026). CANNs: Continuous Attractor Neural Networks Toolkit (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.18453893
+
 ## Contributing & License
 
 Contributions are welcome. Please read [CONTRIBUTING.md](CONTRIBUTING.md) before opening a PR.

{canns-1.0.0 → canns-1.0.1}/README_zh.md

@@ -9,7 +9,7 @@
 [<img src="https://badges.ws/maintenance/yes/2026" />](https://github.com/routhleck/canns)
 <picture><img src="https://badges.ws/github/release/routhleck/canns" /></picture>
 <picture><img src="https://badges.ws/github/license/routhleck/canns" /></picture>
-[![DOI](https://zenodo.org/badge/1001781809.svg)](https://doi.org/10.5281/zenodo.17412545)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18453893.svg)](https://doi.org/10.5281/zenodo.18453893)
 
 
 <picture><img src="https://badges.ws/github/stars/routhleck/canns?logo=github" /></picture>
@@ -26,9 +26,9 @@ CANNs（Continuous Attractor Neural Networks toolkit）是基于 [BrainPy](https
 ## 架构
 
 <p align="center">
-  <img src="images/architecture.png" alt="CANNs Architecture" width="900">
+  <img src="docs/_static/architecture.png" alt="CANNs Architecture" width="900">
   <br>
-  <span style="color: grey; font-size: 14px;">架构概览：模型、任务、分析器、训练器与流水线基于 BrainPy/JAX，部分环节可选 Rust 加速。</span>
+  <span style="color: grey; font-size: 14px;">CANNs 库的层级结构，展示了五个层级：应用层（流水线编排）、功能层（任务、训练器、分析器、工具模块）、核心模型层（CANN 实现）、基础层（BrainPy/JAX 和 Rust FFI 后端）以及硬件层（CPU/GPU/TPU 支持）</span>
 </p>
 
 CANNs 采用模块化架构，遵循两条核心原则：**关注点分离** 与 **通过基类实现可扩展性**。
@@ -62,12 +62,12 @@ CANNs 采用模块化架构，遵循两条核心原则：**关注点分离** 与
 </p>
 
 <p align="center">
-  <img src="images/analyzer-display.png" alt="Analyzer Display" width="900">
+  <img src="docs/_static/analyzer-display.png" alt="Analyzer Display" width="900">
   <br>
   <span style="color: grey; font-size: 14px;">丰富的 Analyzer 可视化结果</span>
 </p>
 <p align="center">
-  <img src="images/asa-gui.gif" alt="ASA GUI Preview" width="720">
+  <img src="docs/_static/asa-gui.gif" alt="ASA GUI Preview" width="720">
   <br>
   <span style="color: grey; font-size: 14px;">ASA GUI 预览</span>
 </p>
@@ -176,12 +176,12 @@ energy_landscape_1d_animation(
 pip install canns
 
 # 可选加速（Linux）
-pip install "canns[cuda12]"
-pip install "canns[cuda13]"
-pip install "canns[tpu]"
+pip install canns[cuda12]
+pip install canns[cuda13]
+pip install canns[tpu]
 
 # GUI（ASA Pipeline）
-pip install "canns[gui]"
+pip install canns[gui]
 ```
 
 可选（uv）：
@@ -198,6 +198,32 @@ uv pip install canns
 - Sphinx 文档与 Notebook：`docs/`
 - ASA GUI 入口：`canns-gui`
 
+## 引用
+
+如果您在研究中使用了 CANNs，请引用：
+
+```bibtex
+@software{he_2026_canns,
+  author       = {He, Sichao and
+                  Tuerhong, Aiersi and
+                  She, Shangjun and
+                  Chu, Tianhao and
+                  Wu, Yuling and
+                  Zuo, Junfeng and
+                  Wu, Si},
+  title        = {CANNs: Continuous Attractor Neural Networks Toolkit},
+  month        = feb,
+  year         = 2026,
+  publisher    = {Zenodo},
+  version      = {v1.0.0},
+  doi          = {10.5281/zenodo.18453893},
+  url          = {https://doi.org/10.5281/zenodo.18453893}
+}
+```
+
+**纯文本格式：**
+> He, S., Tuerhong, A., She, S., Chu, T., Wu, Y., Zuo, J., & Wu, S. (2026). CANNs: Continuous Attractor Neural Networks Toolkit (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.18453893
+
 ## 贡献&许可证
 
 欢迎提交 Issue / PR。请先阅读 [CONTRIBUTING.md](CONTRIBUTING.md)。

{canns-1.0.0 → canns-1.0.1}/pyproject.toml

@@ -64,6 +64,7 @@ dependencies = [
 dev = [
     "pytest>=8.3.5",
     "pytest-sugar>=1.0.0",
+    "pytest-cov>=6.0.0",
     "ruff>=0.11.9",
     "codespell>=2.4.1",
     "rich>=14.0.0",
@@ -116,7 +117,7 @@ gui = [
 
 [project.scripts]
 # Add script entry points here:
-canns = "canns:master"
+canns = "canns.__main__:main"
 canns-tui = "canns.pipeline.launcher:main"
 canns-gallery = "canns.pipeline.gallery:main"
 canns-gui = "canns.pipeline.asa_gui:main"
@@ -245,13 +246,31 @@ reportOperatorIssue = false
 # skip = "foo.py,bar.py"
 
 [tool.pytest.ini_options]
-python_files = ["*.py"]
+python_files = ["test_*.py"]
 python_classes = ["Test*"]
 python_functions = ["test_*"]
 testpaths = [
-    "src",
     "tests",
 ]
 norecursedirs = []
 filterwarnings = []
-addopts = "--assert=plain"
+addopts = "--assert=plain -ra"
+markers = [
+    "integration: tests that exercise multi-module flows or external dependencies",
+    "visualization: tests that generate plots or graphics",
+    "slow: tests that are notably slower than unit tests",
+]
+
+[tool.coverage.run]
+branch = true
+source = ["canns"]
+
+[tool.coverage.report]
+skip_covered = true
+show_missing = true
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+    "if __name__ == .__main__.:",
+    "raise NotImplementedError",
+]

{canns-1.0.0 → canns-1.0.1}/src/canns/__init__.py

@@ -11,12 +11,10 @@ Examples:
     >>> print(list(canns.data.DATASETS))
 """
 
-from . import analyzer as analyzer
-from . import data as data
-from . import models as models
-from . import pipeline as pipeline
-from . import trainer as trainer
-from . import utils as utils
+from __future__ import annotations
+
+import importlib
+from typing import TYPE_CHECKING
 
 # Version information
 try:
@@ -49,6 +47,27 @@ Examples:
     >>> print(canns.version_info)
 """
 
+_LAZY_SUBMODULES = {
+    "analyzer",
+    "data",
+    "models",
+    "pipeline",
+    "trainer",
+    "utils",
+}
+
+if TYPE_CHECKING:  # pragma: no cover
+    from . import analyzer, data, models, pipeline, trainer, utils
+
+
+def __getattr__(name: str):
+    if name in _LAZY_SUBMODULES:
+        module = importlib.import_module(f"{__name__}.{name}")
+        globals()[name] = module
+        return module
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+
 __all__ = [
     "analyzer",
     "data",

canns-1.0.1/src/canns/__main__.py

@@ -0,0 +1,69 @@
+"""Command-line entry point for the CANNs toolkit.
+
+`pip/uv install canns` installs several console scripts:
+- `canns`: convenience wrapper (this module)
+- `canns-tui`: Textual launcher (ASA / Gallery)
+- `canns-gallery`: Gallery TUI
+- `canns-gui`: ASA GUI (requires `canns[gui]`)
+"""
+
+from __future__ import annotations
+
+import argparse
+import sys
+from collections.abc import Sequence
+
+
+def main(argv: Sequence[str] | None = None) -> int:
+    parser = argparse.ArgumentParser(prog="canns", description="CANNs toolkit entry point.")
+    parser.add_argument(
+        "--version",
+        action="store_true",
+        help="Print installed CANNs version and exit.",
+    )
+    group = parser.add_mutually_exclusive_group()
+    group.add_argument("--asa", action="store_true", help="Run the ASA TUI directly.")
+    group.add_argument("--gallery", action="store_true", help="Run the model gallery TUI directly.")
+    group.add_argument("--gui", action="store_true", help="Run the ASA GUI (requires canns[gui]).")
+
+    args = parser.parse_args(list(argv) if argv is not None else None)
+
+    if args.version:
+        try:
+            from importlib.metadata import version
+
+            print(version("canns"))
+        except Exception:
+            try:
+                from canns._version import __version__
+
+                print(__version__)
+            except Exception:
+                print("unknown")
+        return 0
+
+    if args.gui:
+        from canns.pipeline.asa_gui import main as gui_main
+
+        return int(gui_main())
+
+    if args.gallery:
+        from canns.pipeline.gallery import main as gallery_main
+
+        gallery_main()
+        return 0
+
+    if args.asa:
+        from canns.pipeline.asa import main as asa_main
+
+        asa_main()
+        return 0
+
+    from canns.pipeline.launcher import main as launcher_main
+
+    launcher_main()
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main(sys.argv[1:]))

{canns-1.0.0 → canns-1.0.1}/src/canns/analyzer/data/asa/cohospace_scatter.py

@@ -10,7 +10,6 @@ from ...visualization.core import PlotConfig, finalize_figure
 from .path import _align_activity_to_coords, skew_transform
 from .utils import _ensure_parent_dir, _ensure_plot_config
 
-
 # =====================================================================
 # CohoSpace visualization and selectivity metrics (CohoScore)
 # =====================================================================

{canns-1.0.0 → canns-1.0.1}/src/canns/analyzer/data/cell_classification/visualization/btn_plots.py

@@ -2,8 +2,6 @@
 
 from __future__ import annotations
 
-from typing import Any
-
 import numpy as np
 from matplotlib import pyplot as plt
 from scipy.ndimage import gaussian_filter1d