j-brady/peakipy

Interactive NMR peak deconvolution

peakipy's Issues

Please switch license from GPL to LGPL

The project is licensed under GPL which is not intended for libraries, the LGPL is. The consequence of this is that legally non-GPL open source licensed applications (Like BSD, Apache, MIT, and virtually every open-source license other than GPL) can not use this library as a dependency. This makes it impossible for most projects to use the library at all as a dependency.

Potential dependency conflicts between peakipy and numpy

Hi, as shown in the following full dependency graph of peakipy, peakipy requires numpy >=1.16,<2.0, numdifftools requires statsmodels >=0.6 (statsmodels 0.11.1 will be installed, i.e., the newest version satisfying the version constraint), and directed dependency statsmodels 0.11.1 transitively introduces numpy >=1.2.0,<1.3.0.

Obviously, there are multiple version constraints set for numpy in this project. However, according to pip's “first found wins” installation strategy, numpy 1.19.0rc1 (i.e., the newest version satisfying constraint >=1.16,<2.0) is the actually installed version.

Although the first found package version numpy 1.19.0rc1 just satisfies the later dependency constraint （numpy >=1.16,<2.0), such installed version is very close to the upper bound of the version constraint of numpy specified by statsmodels 0.11.1.

Once _statsmodels _ upgrades，its newest version will be installed, as peakipy does not specify the upper bound of version constraint for _statsmodels _. Therefore, it will easily cause a dependency conflict (build failure), if the upgraded _statsmodels _ version introduces a higher version of numpy, violating its another version constraint >=1.16,<2.0.

According to the release history of statsmodels , it habitually upgrates Numpy in its recent releases. For instance, statsmodels 0.10.0rc1 upgrated Numpy’s constraint from >=1.09 to >=1.11,statsmodels 0.11.0rc1 upgrated Numpy’s constraint from >=1.11 to >=1.14 and statsmodels next version upgrated Numpy’s constraint from >=1.14 to >=1.15.

As such, it is a warm warning of a potential dependency conflict issue for peakipy.

Dependency tree

peakipy - 0.1.29
| +- bokeh(install version:1.4.0 version range:>=1.0.4,<2.0.0)
| | +- jinja2(install version:2.11.2 version range:>=2.7)
| | | +- MarkupSafe(install version:2.0.0a1 version range:>=0.23)
| | +- numpy(install version:1.19.0rc1 version range:>=1.7.1)
| | +- packaging(install version:20.3 version range:>=16.8)
| | +- pillow(install version:7.1.1 version range:>=4.0)
| | +- python-dateutil(install version:2.8.1 version range:>=2.1)
| | +- pyyaml(install version:5.3.1 version range:>=3.10)
| | +- six(install version:1.14.0 version range:>=1.5.2)
| | +- tornado(install version:6.0.4 version range:>=4.3)
| +- colorama(install version:0.4.3 version range:>=0.4.1,<0.5.0)
| +- docopt(install version:0.6.2 version range:>=0.6.2,<0.7.0)
| +- lmfit(install version:0.9.15 version range:>=0.9.12,<0.10.0)
| | +- asteval(install version:0.9.18 version range:>=0.9.16)
| | +- numpy(install version:1.19.0rc1 version range:>=1.16)
| | +- scipy(install version:1.4.1 version range:>=1.2)
| | +- six(install version:1.14.0 version range:>=1.11)
| | +- uncertainties(install version:3.1.2 version range:>=3.0.1)
| +- matplotlib(install version:3.2.1 version range:>=3.0,<4.0)
| | +- cycler(install version:0.10.0 version range:>=0.10)
| | | +- six(install version:1.14.0 version range:*)
| | +- kiwisolver(install version:1.2.0 version range:>=1.0.1)
| | +- numpy(install version:1.19.0rc1 version range:>=1.11)
| | +- pyparsing(install version:3.0.0a1 version range:>=2.0.1)
| | +- python-dateutil(install version:2.8.1 version range:>=2.1)
| +- nmrglue(install version:0.6 version range:>=0.6.0,<0.7.0)
| | +- numpy(install version:1.19.0rc1 version range:*)
| | +- scipy(install version:1.4.1 version range:*)
| +- numba(install version:0.44.1 version range:>=0.44.1,<0.45.0)
| +- numdifftools(install version:0.9.39 version range:>=0.9.39,<0.10.0)
| | +- algopy(install version:0.5.7 version range:>=0.4)
| | +- numpy(install version:1.19.0rc1 version range:>=1.9)
| | +- scipy(install version:1.4.1 version range:>=0.8)
| | +- statsmodels(install version:0.11.1 version range:>=0.6)
| | | +- numpy(install version:1.19.0rc1 version range:>=1.14)
| | | +- pandas(install version:0.24.2 version range:>=0.21)
| | | +- patsy(install version:0.5.1 version range:>=0.5)
| | | | +- numpy(install version:1.19.0rc1 version range:>=1.4)
| | | | +- six(install version:1.14.0 version range:*)
| | | +- scipy(install version:1.4.1 version range:>=1.0)
| +- numpy(install version:1.19.0rc1 version range:>=1.16,<2.0)
| +- pandas(install version:0.24.2 version range:>=0.24.0,<0.25.0)
| +- PyYAML(install version:5.3.1 version range:>=5.1,<6.0)
| +- schema(install version:0.7.2 version range:>=0.7.0,<0.8.0)
| | +- contextlib2(install version:0.6.0.post1 version range:>=0.5.5)
| +- scikit-image(install version:0.14.5 version range:>=0.14.2,<0.15.0)
| +- scipy(install version:1.4.1 version range:>=1.2,<2.0)
| +- tabulate(install version:0.8.7 version range:>=0.8.3,<0.9.0)

Thanks for your help.
Best,
Neolith

Potential dependency conflicts between peakipy and pandas

Hi, as shown in the following full dependency graph of peakipy, peakipy requires pandas >=0.24.0,<0.25.0, numdifftools requires statsmodels >=0.6 (statsmodels 0.11.1 will be installed, i.e., the newest version satisfying the version constraint), and directed dependency statsmodels 0.11.1 transitively introduces pandas >=0.21.

Obviously, there are multiple version constraints set for pandas in this project. However, according to pip's “first found wins” installation strategy, pandas 0.24.2 (i.e., the newest version satisfying constraint >=0.24.0,<0.25.0) is the actually installed version.

Although the first found package version pandas 0.24.2 just satisfies the later dependency constraint （pandas >=0.24.0,<0.25.0), such installed version is very close to the upper bound of the version constraint of pandas specified by statsmodels 0.11.1.

Once _statsmodels _ upgrades，its newest version will be installed, as peakipy does not specify the upper bound of version constraint for _statsmodels _. Therefore, it will easily cause a dependency conflict (build failure), if the upgraded _statsmodels _ version introduces a higher version of pandas, violating its another version constraint >=0.24.0,<0.25.0.

According to the release history of statsmodels , it habitually upgrates Pandas in its recent releases. For instance, statsmodels 0.10.0rc2 upgrated Pandas’s constraint from >=0.18 to >=0.19 ,statsmodels 0.11.0rc1 upgrated Pandas’s constraint from >=0.19 to >=0.21 and statsmodels next version upgrated Pandas’s constraint from >=0.21 to >=0.23.

As such, it is a warm warning of a potential dependency conflict issue for peakipy.

Dependency tree

peakipy - 0.1.29
| +- bokeh(install version:1.4.0 version range:>=1.0.4,<2.0.0)
| | +- jinja2(install version:2.11.2 version range:>=2.7)
| | | +- MarkupSafe(install version:2.0.0a1 version range:>=0.23)
| | +- pandas(install version:0.24.2 version range:>=1.7.1)
| | +- packaging(install version:20.3 version range:>=16.8)
| | +- pillow(install version:7.1.1 version range:>=4.0)
| | +- python-dateutil(install version:2.8.1 version range:>=2.1)
| | +- pyyaml(install version:5.3.1 version range:>=3.10)
| | +- six(install version:1.14.0 version range:>=1.5.2)
| | +- tornado(install version:6.0.4 version range:>=4.3)
| +- colorama(install version:0.4.3 version range:>=0.4.1,<0.5.0)
| +- docopt(install version:0.6.2 version range:>=0.6.2,<0.7.0)
| +- lmfit(install version:0.9.15 version range:>=0.9.12,<0.10.0)
| | +- asteval(install version:0.9.18 version range:>=0.9.16)
| | +- pandas(install version:0.24.2 version range:>=1.16)
| | +- scipy(install version:1.4.1 version range:>=1.2)
| | +- six(install version:1.14.0 version range:>=1.11)
| | +- uncertainties(install version:3.1.2 version range:>=3.0.1)
| +- matplotlib(install version:3.2.1 version range:>=3.0,<4.0)
| | +- cycler(install version:0.10.0 version range:>=0.10)
| | | +- six(install version:1.14.0 version range:*)
| | +- kiwisolver(install version:1.2.0 version range:>=1.0.1)
| | +- pandas(install version:0.24.2 version range:>=1.11)
| | +- pyparsing(install version:3.0.0a1 version range:>=2.0.1)
| | +- python-dateutil(install version:2.8.1 version range:>=2.1)
| +- nmrglue(install version:0.6 version range:>=0.6.0,<0.7.0)
| | +- pandas(install version:0.24.2 version range:*)
| | +- scipy(install version:1.4.1 version range:*)
| +- numba(install version:0.44.1 version range:>=0.44.1,<0.45.0)
| +- numdifftools(install version:0.9.39 version range:>=0.9.39,<0.10.0)
| | +- algopy(install version:0.5.7 version range:>=0.4)
| | +- pandas(install version:0.24.2 version range:>=1.9)
| | +- scipy(install version:1.4.1 version range:>=0.8)
| | +- statsmodels(install version:0.11.1 version range:>=0.6)
| | | +- pandas(install version:0.24.2 version range:>=1.14)
| | | +- pandas(install version:0.24.2 version range:>=0.21)
| | | +- patsy(install version:0.5.1 version range:>=0.5)
| | | | +- pandas(install version:0.24.2 version range:>=1.4)
| | | | +- six(install version:1.14.0 version range:*)
| | | +- scipy(install version:1.4.1 version range:>=1.0)
| +- pandas(install version:0.24.2 version range:>=0.24.0,<0.25.0)
| +- pandas(install version:0.24.2 version range:>=0.24.0,<0.25.0)
| +- PyYAML(install version:5.3.1 version range:>=5.1,<6.0)
| +- schema(install version:0.7.2 version range:>=0.7.0,<0.8.0)
| | +- contextlib2(install version:0.6.0.post1 version range:>=0.5.5)
| +- scikit-image(install version:0.14.5 version range:>=0.14.2,<0.15.0)
| +- scipy(install version:1.4.1 version range:>=1.2,<2.0)
| +- tabulate(install version:0.8.7 version range:>=0.8.3,<0.9.0)

Thanks for your help.
Best,
Neolith