Merge pull request #60 from LooseLab/issue59

Windows installation issues with strict requirements and missing subpackages
LooseLab · Jun 28, 2023 · 63c2e17 · 63c2e17
2 parents 00a82a9 + ea87c3b
commit 63c2e17
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Showing 5 changed files with 35 additions and 17 deletions.
diff --git a/README.md b/README.md
@@ -5,23 +5,36 @@ An app written in Python3 using [Bokeh][1] to visualise raw squiggle data from O
 
 Quickstart
 ==========
-We require python 3.6 or newer.
 
-Using `conda` with this environment setup:
+Our preferred installation method uses `conda` with this environment setup:
 ```yaml
 name: bulkvis
 channels:
   - bioconda
   - conda-forge
   - defaults
 dependencies:
-  - python=3.7
+  - python=3.11
   - pip
   - pip:
     - git+https://github.com/LooseLab/bulkvis.git@2.0
 ```
 
-or with another python source:
+Either copy the YAML above into a file or:
+
+```console
+curl -O https://raw.githubusercontent.com/LooseLab/bulkvis/2.0/env.yml
+conda env create -f env.yml
+```
+
+Then bulkvis can be started using:
+```console
+conda activate bulkvis
+bulkvis serve <BULK_FILE_DIRECTORY> --show
+```
+
+<details>
+<summary>or with another python source</summary>
 
 ```bash
 # Make a python3 virtual environment
@@ -36,6 +49,7 @@ pip install git+https://github.com/LooseLab/bulkvis.git@2.0
 # Start bokeh server
 bulkvis serve <BULK_FILE_DIRECTORY> --show
 ```
+</details>
 
 Other install requires:
 ===

diff --git a/bulkvis/_version.py b/bulkvis/_version.py
@@ -1 +1 @@
-__version__ = "2.0.0a5"
+__version__ = "2.0.1"
diff --git a/env.yml b/env.yml
@@ -0,0 +1,10 @@
+name: bulkvis
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.11
+  - pip
+  - pip:
+    - git+https://github.com/LooseLab/bulkvis.git
diff --git a/requirements.txt b/requirements.txt
diff --git a/setup.py b/setup.py
@@ -5,11 +5,11 @@
     exec(fh.read(), version)
 
 install_requires = [
-    "bokeh~=2.1.0",
-    "h5py~=2.10.0",
-    "pandas~=1.0.5",
-    "tornado~=6.0.4",
-    "tqdm~=4.46.1",
+    "bokeh>=2.1.0,<2.4.0",
+    "h5py",
+    "pandas>1.0,<2.0",
+    "tornado",
+    "tqdm",
     "readpaf",
 ]
 
@@ -23,7 +23,7 @@
             "bulkvis=bulkvis.bulkvis:main",
         ],
     },
-    packages=["bulkvis"],
+    packages=["bulkvis", "bulkvis.bulkvis_server"],
     python_requires=">=3.6",
     include_package_data=True,
 )