Merge pull request #9 from spectrochempy/master

calculation of the xaxis + travis/conda configs

.gitignore

@@ -1,2 +1,7 @@
 *.pyc
 *.csv
+
+# dir
+.idea/
+conda-bld/
+*.egg-info/

.travis.yml

@@ -0,0 +1,32 @@
+language: python
+
+python:
+  - "3.7"
+
+# limit git clone depth to 50 commits
+git:
+  depth: 50
+
+install:
+  - sudo apt-get update
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - source "$HOME/miniconda/etc/profile.d/conda.sh"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  - conda config --add channels conda-forge
+  - conda config --add channels spectrocat
+  - conda config --set channel_priority strict
+
+script:
+  - conda create -n py$TRAVIS_PYTHON_VERSION python=$TRAVIS_PYTHON_VERSION pytest numpy scipy
+  - conda activate py$TRAVIS_PYTHON_VERSION
+  - conda update pytest
+  - pip install .
+  - pytest
+
+after_success:
+  - conda activate py$TRAVIS_PYTHON_VERSION
+  - conda install conda-build anaconda-client
+  - bash recipe/conda_upload.sh

brukeropusreader/opus_data.py

@@ -7,8 +7,8 @@ class OpusData(dict):
         param_key = f"{spec_name} Data Parameter"
         fxv = self[param_key]["FXV"]
         lxv = self[param_key]["LXV"]
-        # NPT and REAL NUMBER OF POINTS may differ
+        # the number of points here is OK. It is "AB" that can return more values (equals to zero)
-        npt = self[spec_name].shape[0]
+        npt = self[param_key]["NPT"]
         x_no_unit = np.linspace(fxv, lxv, npt)
         if wavenums:
             return x_no_unit

example.py

@@ -11,14 +11,17 @@ def main(path_to_file):
     print(f"Data fields: " f"{list(opus_data.keys())}")
 
     ab_x = opus_data.get_range("AB")
+    # the "AB" data can contain more null values at the end (at least 1)
+    # so the getting useful data requires slicing the array:
+    abs = opus_data["AB"][0:len(ab_x)]
     print(f"Absorption spectrum range: " f"{ab_x[0]} {ab_x[-1]}")
-    print(f"Absorption elements num: " f'{len(opus_data["AB"])}')
+    print(f"Absorption elements num: " f'{len(abs)}')
 
     try:
         import matplotlib.pyplot as plt
 
         print("Plotting AB")
-        plt.plot(opus_data.get_range("AB"), opus_data["AB"])
+        plt.plot(opus_data.get_range("AB"), abs)
         plt.show()
 
         print("Plotting interpolated AB")

recipe/conda_upload.sh

@@ -0,0 +1,91 @@
+#!/usr/bin/env bash
+
+## adapted on https://gist.github.com/zshaheen/fe76d1507839ed6fbfbccef6b9c13ed9
+
+PKG_NAME=brukeropusreader
+OS=noarch
+conda config --set anaconda_upload no
+
+## TAG
+TAG=$(git describe --tags)
+IFS=$"-"
+read -ra arr <<< "$TAG"
+LAST_TAG="${arr[0]}"
+IFS=$"."
+read -ra tag <<< "$LAST_TAG"
+NEXT_TAG="${tag[0]}.${tag[1]}.`expr ${tag[2]} + 1`"
+NUMBER="${arr[1]}"
+
+export CONDA_BLD_PATH="$HOME/conda-bld"
+mkdir -p "$CONDA_BLD_PATH"
+
+## Here we will choose depending on the way this script is run
+if [[ $USER != "travis" ]]; then
+  ## if we are in local
+  TRAVIS_BRANCH=$(git rev-parse --abbrev-ref HEAD)
+  if [[ $TRAVIS_BRANCH == $LAST_TAG ]]; then
+    TRAVIS_TAG=$LAST_TAG
+  fi
+  ## else this run by TravisCI (this are env variables)
+fi
+
+echo "user: $USER   current branch: $TRAVIS_BRANCH last_tag: $LAST_TAG next_tag: $NEXT_TAG"
+
+if [[ $TRAVIS_BRANCH == "master" ]]; then
+  ## we build the current master repository (i.e.the last development version)
+  export DEVSTRING="latest"
+  export VERSION="$NEXT_TAG"
+  echo "***************************************************************************************************************"
+  echo "--> BUILDING $CONDA_BLD_PATH/$OS/$PKG_NAME-$VERSION-$DEVSTRING.tar.bz2"
+  echo "***************************************************************************************************************"
+  conda build .
+  echo "***************************************************************************************************************"
+  echo "--> UPLOADING $CONDA_BLD_PATH/$OS/$PKG_NAME-$VERSION-$DEVSTRING.tar.bz2 to <dev> anaconda repository"
+  echo "***************************************************************************************************************"
+  anaconda -t "$CONDA_UPLOAD_TOKEN" upload --force -u $ANACONDA_USER -l dev "$CONDA_BLD_PATH/$OS/$PKG_NAME-$VERSION-$DEVSTRING.tar.bz2"
+  exit $?
+fi
+
+if [[ $TRAVIS_BRANCH == $TRAVIS_TAG ]]; then
+  ## this is a "stable" release
+  export DEVSTRING="stable"
+  export VERSION="$LAST_TAG"
+  echo "***************************************************************************************************************"
+  echo "--> BUILDING $CONDA_BLD_PATH/$OS/$PKG_NAME-$VERSION-$DEVSTRING.tar.bz2"
+  echo "***************************************************************************************************************"
+  conda build .
+  echo "***************************************************************************************************************"
+  echo "--> UPLOADING $CONDA_BLD_PATH/$OS/$PKG_NAME-$VERSION-$DEVSTRING.tar.bz2 to <main> anaconda repository"
+  echo "***************************************************************************************************************"
+  anaconda -t "$CONDA_UPLOAD_TOKEN" upload --force -u $ANACONDA_USER  "$CONDA_BLD_PATH/$OS/$PKG_NAME-$VERSION-$DEVSTRING.tar.bz2"
+  exit $?
+fi
+
+if [ ! $NUMBER ]
+then
+   NUMBER="0"
+fi
+
+if [[ $TRAVIS_BRANCH == "develop" ]]; then
+  ## we build the current develop repository (for testing purpose)
+  export DEVSTRING="test$NUMBER"
+  export VERSION="$NEXT_TAG"
+  echo "***************************************************************************************************************"
+  echo "--> BUILDING $CONDA_BLD_PATH/$OS/$PKG_NAME-$VERSION-$DEVSTRING.tar.bz2"
+  echo "***************************************************************************************************************"
+  conda build .
+  echo "***************************************************************************************************************"
+  echo "--> UPLOADING $CONDA_BLD_PATH/$OS/$PKG_NAME-$VERSION-$DEVSTRING.tar.bz2 to <test> anaconda repository"
+  echo "***************************************************************************************************************"
+  anaconda -t "$CONDA_UPLOAD_TOKEN" upload --force -u $ANACONDA_USER -l test "$CONDA_BLD_PATH/$OS/$PKG_NAME-$VERSION-$DEVSTRING.tar.bz2"
+  exit $?
+fi
+
+## this is a local "dev" release not yet merged with develop (will not be uploaded)
+export DEVSTRING="test$NUMBER"
+export VERSION="$NEXT_TAG"
+echo "***************************************************************************************************************"
+echo "--> BUILDING $CONDA_BLD_PATH/$OS/$PKG_NAME-$VERSION-$DEVSTRING.tar.bz2"
+echo "***************************************************************************************************************"
+conda build .
+exit $?

recipe/meta.yaml

@@ -0,0 +1,52 @@
+{% set name = "brukeropusreader" %}
+{% set version = environ['VERSION'] %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  path: ../
+
+build:
+  script_env:
+    - VERSION
+    - CONDA_BLD_PATH
+  string: {{ environ['DEVSTRING'] }}
+  noarch: python
+  script: "{{ PYTHON }} -m pip install . -vv"
+
+requirements:
+  build:
+    - python
+  host:
+    - python
+    - numpy
+    - pip
+    - scipy
+  run:
+    - python
+    - numpy
+    - scipy
+  test:
+    - python             {{ python }}
+    - pytest
+
+test:
+  script_env:
+    - VERSION
+    - CONDA_BLD_PATH
+  imports:
+    - brukeropusreader
+
+about:
+  home: "https://github.com/spectrochempy/brukeropusreader"
+  license: GPLv3
+  license_family: GPL3
+  summary: "Bruker OPUS File Reader"
+  doc_url: "https://github.com/spectrochempy/brukeropusreader"
+  dev_url: "https://github.com/spectrochempy/brukeropusreader"
+
+extra:
+  recipe-maintainers:
+    - fernandezc

requirements.in

@@ -1,3 +0,0 @@
-numpy
-scipy
-

requirements.txt

@@ -1,8 +0,0 @@
-#
-# This file is autogenerated by pip-compile
-# To update, run:
-#
-#    pip-compile --output-file=requirements.txt requirements.in
-#
-numpy==1.16.1
-scipy==1.2.1

setup.py

@@ -1,14 +1,13 @@
-from distutils.core import setup
+from setuptools import setup
-
 
 setup(
     name="brukeropusreader",
-    version="1.3.4",
+    use_scm_version=True,
     description="Bruker OPUS File Reader",
     author="QED",
     author_email="brukeropusreader-dev@qed.ai",
     packages=["brukeropusreader"],
-    install_requires=["numpy>=1.13.3", "scipy>=0.19.1"],
+    # install_requires=["numpy>=1.13.3", "scipy>=0.19.1"],
     license="GPLv3",
     url="https://github.com/qedsoftware/brukeropusreader",
 )

tests/test_import.py

@@ -0,0 +1,5 @@
+def test_import():
+    import brukeropusreader as bor
+    l = dir(bor)
+    assert 'opus_reader' in l
+