16/57: gnu: Remove work-arounds for bug 20765 (ensure uncompressed eggs).

2016-10-15 Thread Hartmut Goebel 
htgoebel pushed a commit to branch wip-python-build-system
in repository guix.

commit 3ac6bbdab10572e5ae616d6ba3b7ff90f77b6592
Author: Hartmut Goebel 
Date:   Wed Sep 28 15:23:10 2016 +0200

gnu: Remove work-arounds for bug 20765 (ensure uncompressed eggs).

Bug 20765 is solved since we build all Python packages using
option "--single-version-externally-managed".

* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove
  configure-flags. (pepr): remove phase "disable-egg-generation".
* gnu/packages/pdf.scm (reportlab): Remove configure-flags.
* gnu/packages/python.scm (python-sphinx-rtd-theme, python2-elib.intl,
  python-pkgconfig, python-pytest-pep8, python-pytest-flakes): Remove
  configure-flags. (python-pillow) remove phase
  "disable-egg-generation". (python-libarchive-c) Remove patching
  setup.cfg.
* gnu/packages/statistics.scm (python-patsy): remove phase
  "prevent-generation-of-egg-archive".
* gnu/packages/tls.scm (python-acme): remove phase
  "disable-egg-compression".
* gnu/packages/tor.scm (onionshare): Remove configure-flags.
---
 gnu/packages/bioinformatics.scm |   19 +---
 gnu/packages/pdf.scm|5 -
 gnu/packages/python.scm |   47 ---
 gnu/packages/statistics.scm |8 +--
 gnu/packages/tls.scm|9 
 gnu/packages/tor.scm|6 +
 6 files changed, 7 insertions(+), 87 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d1572e2..1ffc848 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3553,11 +3553,6 @@ the phenotype as it models the data.")
   (build-system python-build-system)
   (arguments
`(#:python ,python-2
- ;; With standard flags, the install phase attempts to create a zip'd
- ;; egg file, and fails with an error: 'ZIP does not support timestamps
- ;; before 1980'
- #:configure-flags '("--single-version-externally-managed"
- "--record=pbtranscript-tofu.txt")
  #:phases
  (modify-phases %standard-phases
(add-after 'unpack 'enter-directory
@@ -7282,19 +7277,7 @@ may optionally be provided to further inform the 
peak-calling process.")
 (build-system python-build-system)
 (arguments
  `(#:python ,python-2 ; python2 only
-   #:tests? #f ; no tests included
-   #:phases
-   (modify-phases %standard-phases
- ;; When setuptools is used a ".egg" archive is generated and
- ;; installed.  This makes it hard to actually run PePr.  This issue
- ;; has been reported upstream:
- ;; https://github.com/shawnzhangyx/PePr/issues/9
- (add-after 'unpack 'disable-egg-generation
-   (lambda _
- (substitute* "setup.py"
-   (("from setuptools import setup")
-"from distutils.core import setup"))
- #t)
+   #:tests? #f)) ; no tests included
 (propagated-inputs
  `(("python2-numpy" ,python2-numpy)
("python2-scipy" ,python2-scipy)
diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index 614816f..c8a6e05 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -622,11 +622,6 @@ using a stylus.")
(base32
 "0rz2pg04wnzjjm2f5a8ik9v8s54mv4xrjhv5liqjijqv6awh12gl"
 (build-system python-build-system)
-(arguments
- ;; Prevent creation of the egg. Without this flag, various artifacts
- ;; from the build inputs end up in the final python3 output. It also
- ;; works around https://debbugs.gnu.org/cgi/bugreport.cgi?bug=20765 .
- `(#:configure-flags '("--single-version-externally-managed" "--root=/")))
 (propagated-inputs
  `(("python-pillow" ,python-pillow)))
 (home-page "http://www.reportlab.com;)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index cbbee95..62d5dc9 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -2698,12 +2698,6 @@ sources.")
 (base32
  "19nw3rn7awplcdrz63kg1njqwkbymfg9lwn7l2grhdyhyr2gaa8g"
 (build-system python-build-system)
-(arguments
- `(;; With standard flags, the install phase attempts to create a zip'd
-   ;; egg file, and fails with an error: 'ZIP does not support timestamps
-   ;; before 1980'
-   #:configure-flags '("--single-version-externally-managed"
-   "--record=sphinx-rtd-theme.txt")))
 (inputs
  `(("python-docutils" ,python-docutils)
("python-sphinx" ,python-sphinx)))
@@ -3738,12 +3732,7 @@ Python's distutils.")
 (arguments
  ;; incompatible with Python 3 (exception syntax)
  `(#:python ,python-2
-   #:tests? #f
-   ;; With standard flags, the install phase attempts to create a zip'd
-   ;; egg file, and

16/57: gnu: Remove work-arounds for bug 20765 (ensure uncompressed eggs).

2016-10-13 Thread Hartmut Goebel 
htgoebel pushed a commit to branch wip-python-build-system
in repository guix.

commit c27e06c6994540b70d0adf830b1c292253823c0f
Author: Hartmut Goebel 
Date:   Wed Sep 28 15:23:10 2016 +0200

gnu: Remove work-arounds for bug 20765 (ensure uncompressed eggs).

Bug 20765 is solved since we build all Python packages using
option "--single-version-externally-managed".

* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove
  configure-flags. (pepr): remove phase "disable-egg-generation".
* gnu/packages/pdf.scm (reportlab): Remove configure-flags.
* gnu/packages/python.scm (python-sphinx-rtd-theme, python2-elib.intl,
  python-pkgconfig, python-pytest-pep8, python-pytest-flakes): Remove
  configure-flags. (python-pillow) remove phase
  "disable-egg-generation". (python-libarchive-c) Remove patching
  setup.cfg.
* gnu/packages/statistics.scm (python-patsy): remove phase
  "prevent-generation-of-egg-archive".
* gnu/packages/tls.scm (python-acme): remove phase
  "disable-egg-compression".
* gnu/packages/tor.scm (onionshare): Remove configure-flags.
---
 gnu/packages/bioinformatics.scm |   19 +---
 gnu/packages/pdf.scm|5 -
 gnu/packages/python.scm |   47 ---
 gnu/packages/statistics.scm |8 +--
 gnu/packages/tls.scm|9 
 gnu/packages/tor.scm|6 +
 6 files changed, 7 insertions(+), 87 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d1572e2..1ffc848 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3553,11 +3553,6 @@ the phenotype as it models the data.")
   (build-system python-build-system)
   (arguments
`(#:python ,python-2
- ;; With standard flags, the install phase attempts to create a zip'd
- ;; egg file, and fails with an error: 'ZIP does not support timestamps
- ;; before 1980'
- #:configure-flags '("--single-version-externally-managed"
- "--record=pbtranscript-tofu.txt")
  #:phases
  (modify-phases %standard-phases
(add-after 'unpack 'enter-directory
@@ -7282,19 +7277,7 @@ may optionally be provided to further inform the 
peak-calling process.")
 (build-system python-build-system)
 (arguments
  `(#:python ,python-2 ; python2 only
-   #:tests? #f ; no tests included
-   #:phases
-   (modify-phases %standard-phases
- ;; When setuptools is used a ".egg" archive is generated and
- ;; installed.  This makes it hard to actually run PePr.  This issue
- ;; has been reported upstream:
- ;; https://github.com/shawnzhangyx/PePr/issues/9
- (add-after 'unpack 'disable-egg-generation
-   (lambda _
- (substitute* "setup.py"
-   (("from setuptools import setup")
-"from distutils.core import setup"))
- #t)
+   #:tests? #f)) ; no tests included
 (propagated-inputs
  `(("python2-numpy" ,python2-numpy)
("python2-scipy" ,python2-scipy)
diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index 614816f..c8a6e05 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -622,11 +622,6 @@ using a stylus.")
(base32
 "0rz2pg04wnzjjm2f5a8ik9v8s54mv4xrjhv5liqjijqv6awh12gl"
 (build-system python-build-system)
-(arguments
- ;; Prevent creation of the egg. Without this flag, various artifacts
- ;; from the build inputs end up in the final python3 output. It also
- ;; works around https://debbugs.gnu.org/cgi/bugreport.cgi?bug=20765 .
- `(#:configure-flags '("--single-version-externally-managed" "--root=/")))
 (propagated-inputs
  `(("python-pillow" ,python-pillow)))
 (home-page "http://www.reportlab.com;)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 2a96c06..a7ca1dc 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -2693,12 +2693,6 @@ sources.")
 (base32
  "19nw3rn7awplcdrz63kg1njqwkbymfg9lwn7l2grhdyhyr2gaa8g"
 (build-system python-build-system)
-(arguments
- `(;; With standard flags, the install phase attempts to create a zip'd
-   ;; egg file, and fails with an error: 'ZIP does not support timestamps
-   ;; before 1980'
-   #:configure-flags '("--single-version-externally-managed"
-   "--record=sphinx-rtd-theme.txt")))
 (inputs
  `(("python-docutils" ,python-docutils)
("python-sphinx" ,python-sphinx)))
@@ -3733,12 +3727,7 @@ Python's distutils.")
 (arguments
  ;; incompatible with Python 3 (exception syntax)
  `(#:python ,python-2
-   #:tests? #f
-   ;; With standard flags, the install phase attempts to create a zip'd
-   ;; egg file, and