**Travis CI**
Added a line to install the latest versions of `setuptools` and `importlib-metadata`. Travis-CI Python 3.7 environments contain a very old version of `importlib-metadata` which is incompatible with the majority of libraries for 3.7+.
**Remaining issues**
[ ] Docker builds successfully
**Updating other libraries**
In order for ark-analysis to work with toffy, both toffy and mibi-bin-tools need a couple libraries to be updated.
Order of Updates:
1. Merge angelolab/ark-analysis592 (this one)
2. Merge angelolab/mibi-bin-tools36
3. Merge angelolab/toffy132
</details>
<details>
<summary>Remove GoogleDrivePath Dead Code srivarra (528)</summary>
**If you haven't already, please read through our [contributing guidelines](https://ark-analysis.readthedocs.io/en/latest/_rtd/contributing.html) before opening your PR**
**What is the purpose of this PR?**
Closes 512. Removes all references to `GoogleDrivePath`.
**How did you implement your changes**
All use cases of the Google Drive API in ark-analysis.
- [x] Google Python Packages in the `requirements.txt` and in `setup.py`.
- [x] `data_utils.py`
- [x] Imports `GoogleDrivePath`, `drive_write_out`, `path_join`
- [x] `deepcell_service_utils.py`
- [x] Imports `GoogleDrivePath`, `drive_write_out`, `path_join`, `DriveOpen`
- [x] `google_drive_utils_test.py`
- [x] Delete it
- [x] `google_drive_utils.py`
- [x] Delete it
- [x] `io_utils`
- [x] `load_utils.py`
- [x] `segmentation_utils.py`
- [x] `drive_write_out` and `path_join`
- [x] `conf.py`
- [x] Remove Google packages
- [x] `index.rst`
- [x] Remove GoogleDrive references
- [x] `google_drive_usage.md`
- [x] Remove file
- [x] `Segment_Image_Data.ipynb`
- [x] Uses `deepcell_service_utils.py`.
- [x] Remove Google API tokens
- [ ] Successfully building the Docker Image
**Remaining issues**
None ATM.
</details>
📚️ Documentation
<details>
<summary>Update example\_pixel\_clustering.ipynb ngreenwald (608)</summary>
**If you haven't already, please read through our [contributing guidelines](https://ark-analysis.readthedocs.io/en/latest/_rtd/contributing.html) before opening your PR**
**What is the purpose of this PR?**
Updates the description of additional blurring to more clearly indicate the purpose. Closes 604
</details>
<details>
<summary>Added documentation for setting up development on M1 srivarra (594)</summary>
**If you haven't already, please read through our [contributing guidelines](https://ark-analysis.readthedocs.io/en/latest/_rtd/contributing.html) before opening your PR**
**What is the purpose of this PR?**
Closes 593.
**How did you implement your changes**
Added instructions on getting ark-analysis and running on M1 for development.
**Remaining issues**
This runs under the Intel to Arm transition layer, as we update to Python 3.8, we might want to look at updating libraries to get a native Arm implementation.
</details>
<details>
<summary>Update contributing.md ngreenwald (582)</summary>
**If you haven't already, please read through our [contributing guidelines](https://ark-analysis.readthedocs.io/en/latest/_rtd/contributing.html) before opening your PR**
**What is the purpose of this PR?**
Updates the contributing docs. I noticed that this is now a bit out of date when I sent it to a new collaborator.
**How did you implement your changes**
Updated it to reflect our design doc workflow
</details>
<details>
<summary>adding windows external docs srivarra (564)</summary>
**If you haven't already, please read through our [contributing guidelines](https://ark-analysis.readthedocs.io/en/latest/_rtd/contributing.html) before opening your PR**
**What is the purpose of this PR?**
Closes 562.
Adding an external drive on WSL is a bit ambiguous, so there is now documentation on how to specifically mount an external drive.
**How did you implement your changes**
Added brief documentation based on ackagel 's issue.
**Remaining issues**
None.
</details>
<details>
<summary>Docker Image build instructions, removed rebuild logic srivarra (538)</summary>
**If you haven't already, please read through our [contributing guidelines](https://ark-analysis.readthedocs.io/en/latest/_rtd/contributing.html) before opening your PR**
**What is the purpose of this PR?**
Closes 516.
Placed instructions for building the Docker Image locally in `docs/_rtd/development.md`. Removed the logic which rebuilds the image if changes are detected in `start_docker.sh`.
**How did you implement your changes**
Added instructions based off Installation instructions in the `README.md`. Deleted the logic directly.
**Remaining issues**
None atm.
</details>
<details>
<summary>Documentation for how to run ark-analysis on Windows alex-l-kong (492)</summary>
**What is the purpose of this PR?**
Closes 474 and closes 475. Running `ark-analysis` on Windows requires several extra steps that are not totally intuitive. To provide some hand-holding, create a document on RTD specifically for Windows configuration.
**How did you implement your changes**
Add an RTD page for Windows configuration, which includes WSL, Git, Docker, and carriage-return fixing using `dos2unix`.
**Remaining issues**
If there are any additional issues that other users, including yourself, have encountered on Windows, please let me know.
</details>
ackagel, alex-l-kong, bcollica, camisowers, cliu72, ngreenwald and srivarra