Update telescope (#63719)

* updating to new release

* update SHA for new tarball

* updating package versions to match @marcos-da-conceicao suggestion

here: mlbendall/telescope#57 (comment)

* updating = to ==

* Updating all numpy

* Updating build in recipe

* Adding run_exports statement

* Adding cython to build in recipe

* Updating patch file to specify C compiler, fixing cython linting

* fixing typo in packages

* Adding setuptools back

* Typos

* Updating LDSHARED for macOS

* Typo

* Explicitly adding python3.6m for MacOS

* Trigger build

* Conditional linker arguments for macOS

* Update meta.yaml

* Update meta.yaml

---------

Co-authored-by: Hannah Jones <hannah.18.jones@kcl.ac.uk>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>

Author: hanalysis

recipes/telescope/0001-Fix-setup.py.patch

@@ -1,19 +1,31 @@
---- setup.py
-+++ setup.py
-@@ -5,7 +5,7 @@
+diff --git a/setup.py b/setup.py
+index c856074..a3feaa6 100644
+--- a/setup.py
++++ b/setup.py
+@@ -4,33 +4,44 @@
+ """
  from __future__ import print_function
 
++import os
  from os import path, environ
 -from distutils.core import setup
 +from setuptools import setup
  from setuptools import Extension
  from setuptools import find_packages
+-
+ from telescope._version import VERSION
++import sys
 
-@@ -16,13 +16,13 @@ __copyright__ = "Copyright (C) 2019 Matthew L. Bendall"
+ __author__ = 'Matthew L. Bendall'
+ __copyright__ = "Copyright (C) 2019 Matthew L. Bendall"
 
  USE_CYTHON = True
 
 -CONDA_PREFIX = environ.get("CONDA_PREFIX", '.')
++CC = environ.get('CC', 'gcc')
++os.environ['CC'] = CC
++LDSHARED = environ.get('LDSHARED', CC + ' -shared')
++os.environ['LDSHARED'] = LDSHARED
 +PREFIX = environ.get("PREFIX", '.')
  HTSLIB_INCLUDE_DIR = environ.get("HTSLIB_INCLUDE_DIR", None)
 
@@ -26,3 +38,17 @@
  ]
  htslib_include_dirs = [d for d in htslib_include_dirs if path.exists(str(d)) ]
 
++extra_link_args = []
++if sys.platform == 'darwin':
++    extra_link_args = ['-undefined', 'dynamic_lookup']
++
+ ext = '.pyx' if USE_CYTHON else '.c'
+ extensions = [
+     Extension("telescope.utils.calignment",
+               ["telescope/utils/calignment"+ext],
+               include_dirs=htslib_include_dirs,
++              extra_link_args=extra_link_args,
++              language='c'
+               ),
+ ]
+ 

recipes/telescope/build_failure.linux-64.yaml

@@ -1,44 +1,47 @@
 {% set name = "telescope" %}
-{% set version = "1.0.3" %}
+{% set version = "1.0.3_fix" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  url: https://github.com/mlbendall/telescope/archive/v{{ version }}.tar.gz
-  sha256: 115928f5aa347bf2416a15e9d790744e42553bb1118809b5677788e649269f74
+  url: https://github.com/hanalysis/telescope/archive/v{{ version }}.tar.gz
+  sha256: a508d3598f14e9df888c7fa48f982a59b735b65ab4d15b81a25a202d2af8b2a0
   patches:
     - 0001-Fix-setup.py.patch
 
 build:
-  number: 6
-  skip: True  # [py<30]
-  script: {{ PYTHON }} -m pip install . --no-deps -vv
+  number: 0
+  skip: True  # [py < 30]
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
+  run_exports:
+    - {{ pin_subpackage(name, max_pin=None) }}
 
 requirements:
   build:
     - {{ compiler('c') }}
   host:
     - pip
-    - python
+    - python ==3.6
+    - cython ==0.29.7
     - setuptools
-    - numpy >=1.16.3
-    - scipy >=1.2.1
-    - pysam >=0.15.2
+    - numpy ==1.16.3
+    - scipy ==1.2.1
+    - pysam ==0.15.2
     - future >=0.17.1
     - pyyaml >=5.1
-    - cython
-    - intervaltree
-    - htslib
+    - intervaltree ==3.0.2
+    - htslib ==1.9
+    - pandas ==1.1.3
   run:
-    - python
-    - {{ pin_compatible('numpy') }}
-    - scipy >=1.2.1
-    - pysam >=0.15.2
+    - python ==3.6
+    - numpy ==1.16.3
+    - scipy ==1.2.1
+    - pysam ==0.15.2
     - future >=0.17.1
     - pyyaml >=5.1
-    - intervaltree >=3.0.2
+    - intervaltree ==3.0.2
 
 test:
   commands:
@@ -48,11 +51,12 @@ test:
     - telescope resume -h &> /dev/null
 
 about:
-  home: 'https://github.com/mlbendall/telescope'
+  home: "https://github.com/mlbendall/telescope"
   license: MIT
   license_family: MIT
   license_file: LICENSE
-  summary: Single locus resolution of Transposable ELEment expression.
+  summary: "Single locus resolution of Transposable ELEment expression."
+  dev_url: "https://github.com/mlbendall/telescope"
 
 extra:
   identifiers: