[bug#59239] [PATCH] gnu: Add python-synapseclient.

[bug#59239] [PATCH] gnu: Add python-synapseclient.

[Mădălin Ionel Patrașcu]

* gnu/packages/python-xyz.scm (python-synapseclient): New variable.
---
 gnu/packages/python-xyz.scm | 60 +++++++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e26656fa32..b599a2e4ed 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -10383,6 +10383,66 @@ (define-public python-sympy
 as possible in order to be comprehensible and easily extensible.")
     (license license:bsd-3)))
 
+(define-public python-synapseclient
+  (package
+    (name "python-synapseclient")
+    (version "2.7.0")
+    (source (origin
+              ;; git version contains tests
+              (method git-fetch)
+              (uri (git-reference
+                    (url
+                     "https://github.com/Sage-Bionetworks/synapsePythonClient")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0v2yyjpmxlxmbn1xbxzx1l1bs45ir9p4i51dlf847irnrrmifxcd"))))
+              ;;(method url-fetch)
+              ;;(uri (pypi-uri "synapseclient" version))
+              ;;(sha256
+              ;; (base32
+              ;;  "1g2n5bbq5vkvprk4ap3sbz2q39cjwl8igy3krlskg34c1q7if7r4"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'relax-version-requirements
+           (lambda _
+             (substitute* "setup.py"
+               (("keyring>=15,<23\\.5") "keyring>=15")
+               (("keyrings\\.alt==3\\.1") "keyrings.alt>=3.1"))))
+         (add-before 'build 'set-homeless-shelter
+           (lambda _
+             ;; could not create '/homeless-shelter': Permission denied
+             (setenv "HOME" "/tmp")))
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               ;; these tests require server authentification  SynapseNoCredentialsError
+               (delete-file-recursively "tests/integration/synapseclient")
+               (delete-file-recursively "tests/integration/synapseutils")
+               (invoke "pytest")))))))
+    (propagated-inputs
+     (list python-deprecated
+           python-keyring
+           python-keyrings.alt
+           python-requests))
+    (native-inputs
+     (list python-boto3
+           python-flake8-3.8
+           python-pandas
+           python-psutil
+           python-pytest
+           python-pytest-mock
+           python-pytest-xdist-next))
+    (home-page "https://www.synapse.org")
+    (synopsis "Client for Synapse, a collaborative compute space")
+    (description
+     "This package provides a client for @code{Synapse}, a collaborative compute
+space that allows scientists to share and analyze data together.")
+    (license license:asl2.0)))
+
 (define-public python-q
   (package
     (name "python-q")

base-commit: c4025af8c11c3e9ea0c2747b6c475c916fb61d80
-- 
2.38.1

[bug#59239] [PATCH] gnu: Add python-synapseclient.

[Jonathan Brielmaier]

Hi Mandalin,

I think there are some leftovers included in the patch:
https://issues.guix.gnu.org/59239#0-lineno29

~Jonathan

[bug#59239] [PATCH] gnu: Add python-synapseclient.

[Ricardo Wurmus]

Hi Mădălin,

> * gnu/packages/python-xyz.scm (python-synapseclient): New variable.
[…]

> +              ;;(method url-fetch)
> +              ;;(uri (pypi-uri "synapseclient" version))
> +              ;;(sha256
> +              ;; (base32
> +              ;;  "1g2n5bbq5vkvprk4ap3sbz2q39cjwl8igy3krlskg34c1q7if7r4"))))

Please remove this commented code.

> +    (build-system python-build-system)
> +    (arguments
> +     '(#:phases
> +       (modify-phases %standard-phases
> +         (add-after 'unpack 'relax-version-requirements
> +           (lambda _
> +             (substitute* "setup.py"
> +               (("keyring>=15,<23\\.5") "keyring>=15")

Is this really a good idea?  Upper bounds usually exist for a reason.
We currently have version 23.9.  Can you please clear this with upstream
first?

> +               (("keyrings\\.alt==3\\.1") "keyrings.alt>=3.1"))))
> +         (add-before 'build 'set-homeless-shelter
> +           (lambda _
> +             ;; could not create '/homeless-shelter': Permission denied
> +             (setenv "HOME" "/tmp")))

We’re setting HOME, not homeless-shelter.

> +         (replace 'check
> +           (lambda* (#:key tests? #:allow-other-keys)
> +             (when tests?
> +               ;; these tests require server authentification  SynapseNoCredentialsError
> +               (delete-file-recursively "tests/integration/synapseclient")
> +               (delete-file-recursively "tests/integration/synapseutils")
> +               (invoke "pytest")))))))

typo: “authentication”.  What exactly does this error mean?  Does it
talk to the internet?  How are these tests supposed to be run?

Is it possible to disable these tests with an option to pytest?  That
would seem better than conditionally deleting them.

Finally, I think the test files should be deleted unconditionally, so
that “tests?” only governs whether the tests are *run* instead of also
causing other side effects.

-- 
Ricardo

[bug#59239] [PATCH] gnu: Add python-synapseclient.

[Maxim Cournoyer]

Hello Mădălin,

Ricardo Wurmus <rekado@elephly.net> writes:

> Hi Mădălin,
>
>> * gnu/packages/python-xyz.scm (python-synapseclient): New variable.
> […]
>
>> +              ;;(method url-fetch)
>> +              ;;(uri (pypi-uri "synapseclient" version))
>> +              ;;(sha256
>> +              ;; (base32
>> +              ;;  "1g2n5bbq5vkvprk4ap3sbz2q39cjwl8igy3krlskg34c1q7if7r4"))))
>
> Please remove this commented code.
>
>> +    (build-system python-build-system)
>> +    (arguments
>> +     '(#:phases
>> +       (modify-phases %standard-phases
>> +         (add-after 'unpack 'relax-version-requirements
>> +           (lambda _
>> +             (substitute* "setup.py"
>> +               (("keyring>=15,<23\\.5") "keyring>=15")
>
> Is this really a good idea?  Upper bounds usually exist for a reason.
> We currently have version 23.9.  Can you please clear this with upstream
> first?
>
>> +               (("keyrings\\.alt==3\\.1") "keyrings.alt>=3.1"))))
>> +         (add-before 'build 'set-homeless-shelter
>> +           (lambda _
>> +             ;; could not create '/homeless-shelter': Permission denied
>> +             (setenv "HOME" "/tmp")))
>
> We’re setting HOME, not homeless-shelter.
>
>> +         (replace 'check
>> +           (lambda* (#:key tests? #:allow-other-keys)
>> +             (when tests?
>> +               ;; these tests require server authentification  SynapseNoCredentialsError
>> +               (delete-file-recursively "tests/integration/synapseclient")
>> +               (delete-file-recursively "tests/integration/synapseutils")
>> +               (invoke "pytest")))))))
>
> typo: “authentication”.  What exactly does this error mean?  Does it
> talk to the internet?  How are these tests supposed to be run?
>
> Is it possible to disable these tests with an option to pytest?  That
> would seem better than conditionally deleting them.
>
> Finally, I think the test files should be deleted unconditionally, so
> that “tests?” only governs whether the tests are *run* instead of also
> causing other side effects.

Genle ping.  Could you please send a v2 with the above suggested
changes?

-- 
Thanks,
Maxim