From 28c4d28308756b5e0aa25adde2dfdfe93674e891 Mon Sep 17 00:00:00 2001
From: Charlotte Weaver <charlottesweaver@gmail.com>
Date: Wed, 21 Aug 2019 14:26:01 -0700
Subject: [PATCH] extract prepare from main install (#887)

* extract prepare from main install

* add requirements-prepare to manifest
---
 MANIFEST.in                     |  3 ++-
 server/cli/launch.py            |  5 -----
 server/cli/prepare.py           | 36 +++++++++++++++++++--------------
 server/requirements-prepare.txt |  1 +
 server/requirements.txt         |  4 ----
 setup.py                        |  5 ++++-
 6 files changed, 28 insertions(+), 26 deletions(-)
 create mode 100644 server/requirements-prepare.txt

diff --git a/MANIFEST.in b/MANIFEST.in
index bab7fdc7..6ed38441 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,4 +1,5 @@
 recursive-include server/app/web/templates *
 recursive-include server/app/web/static *
 
-include server/requirements.txt
\ No newline at end of file
+include server/requirements.txt
+include server/requirements-prepare.txt
diff --git a/server/cli/launch.py b/server/cli/launch.py
index 987565a2..2caea22a 100644
--- a/server/cli/launch.py
+++ b/server/cli/launch.py
@@ -185,11 +185,6 @@ def launch(
     else:
         click.echo(f"[cellxgene] Loading data from {basename(data)}.")
 
-    # Fix for anaconda python. matplotlib typically expects python to be installed as a framework TKAgg is usually
-    # available and fixes this issue. See https://matplotlib.org/faq/virtualenv_faq.html
-    import matplotlib as mpl
-
-    mpl.use("TkAgg")
     from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
 
     try:
diff --git a/server/cli/prepare.py b/server/cli/prepare.py
index bad6b18c..b0ff3d43 100644
--- a/server/cli/prepare.py
+++ b/server/cli/prepare.py
@@ -41,18 +41,18 @@ from scipy.sparse.csc import csc_matrix
     "--make-var-names-unique", default=True, is_flag=True, help="Ensure var index is unique.", show_default=True
 )
 def prepare(
-    data,
-    layout,
-    recipe,
-    output,
-    plotting,
-    sparse,
-    overwrite,
-    set_obs_names,
-    set_var_names,
-    run_qc,
-    make_obs_names_unique,
-    make_var_names_unique,
+        data,
+        layout,
+        recipe,
+        output,
+        plotting,
+        sparse,
+        overwrite,
+        set_obs_names,
+        set_var_names,
+        run_qc,
+        make_obs_names_unique,
+        make_var_names_unique,
 ):
     """Preprocesses data for use with cellxgene.
 
@@ -65,10 +65,16 @@ def prepare(
 
     # collect slow imports here to make CLI startup more responsive
     click.echo("[cellxgene] Starting CLI...")
-    import matplotlib
+    try:
+        import matplotlib
 
-    matplotlib.use("Agg")
-    import scanpy as sc
+        matplotlib.use("Agg")
+        import scanpy as sc
+    except ImportError:
+        raise click.ClickException(
+            "[cellxgene] cellxgene prepare has not been installed. Please run `pip install cellxgene[prepare]` "
+            "to install the necessary requirements."
+        )
 
     # scanpy settings
     sc.settings.verbosity = 0
diff --git a/server/requirements-prepare.txt b/server/requirements-prepare.txt
new file mode 100644
index 00000000..d1b43def
--- /dev/null
+++ b/server/requirements-prepare.txt
@@ -0,0 +1 @@
+scanpy>=1.3.7
diff --git a/server/requirements.txt b/server/requirements.txt
index 3c058312..f5bbb00f 100644
--- a/server/requirements.txt
+++ b/server/requirements.txt
@@ -6,11 +6,7 @@ Flask-Compress>=1.4.0
 Flask-Cors>=3.0.6
 Flask-RESTful>=0.3.6
 flatbuffers>=1.10.0
-# TODO revert after scanpy updates their dependency on this
-matplotlib<3.1
 numpy>=1.15.2
 pandas>=0.23.1
-scanpy>=1.3.7
 scipy>=1.1.0
-scikit-learn>=0.19.1,!=0.20.0
 tables==3.5.1
diff --git a/setup.py b/setup.py
index d8b7b75b..7987697d 100644
--- a/setup.py
+++ b/setup.py
@@ -6,6 +6,9 @@ with open("README.md", "rb") as fh:
 with open("server/requirements.txt") as fh:
     requirements = fh.read().splitlines()
 
+with open("server/requirements-prepare.txt") as fh:
+    requirements_prepare = fh.read().splitlines()
+
 setup(
     name="cellxgene",
     version="0.11.0",
@@ -36,5 +39,5 @@ setup(
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],
     entry_points={"console_scripts": ["cellxgene = server.cli.cli:cli"]},
-    extras_require=dict(louvain=["python-igraph", "louvain>=0.6"], gui=["PySide2>=5.12.3", "cefpython3>=66", "requests"]),
+    extras_require=dict(prepare=requirements_prepare, louvain=["python-igraph", "louvain>=0.6"], gui=["PySide2>=5.12.3", "cefpython3>=66", "requests"]),
 )