From c8f6c314ac988cb467ae019f39c290d5e07661ea Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Tue, 19 May 2020 23:23:36 +0200
Subject: [PATCH 01/31] fix install command and publish only once

---
 .github/workflows/conda_publish.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/conda_publish.yml b/.github/workflows/conda_publish.yml
index 480a00c..e53c675 100644
--- a/.github/workflows/conda_publish.yml
+++ b/.github/workflows/conda_publish.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
+        os: ['ubuntu-latest']
         python-version: ['3.7']
     steps:
       - uses: actions/checkout@v2
@@ -69,7 +69,7 @@ jobs:
       - name: Install the conda package from anaconda repository
         shell: bash -l {0}
         run: |
-          conda install conda build -c bioconda -c conda-forge -c nlesc matchms
+          conda install -c bioconda -c conda-forge -c nlesc matchms
       - name: Install development dependencies
         shell: bash -l {0}
         run: python -m pip install -r conda/requirements-dev.txt

From ad56171151442ba23a601f013b7091a806a86b0d Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Tue, 19 May 2020 23:31:22 +0200
Subject: [PATCH 02/31] merge anaconda and python build workflows

---
 .github/workflows/build.yml       | 82 -------------------------------
 .github/workflows/conda_build.yml | 67 +++++++++++++++++++++++++
 2 files changed, 67 insertions(+), 82 deletions(-)
 delete mode 100644 .github/workflows/build.yml

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
deleted file mode 100644
index b08bcfd..0000000
--- a/.github/workflows/build.yml
+++ /dev/null
@@ -1,82 +0,0 @@
-name: 'Python Build'
-
-on: [push, pull_request]
-
-jobs:
-
-  build:
-    name: ${{ matrix.python-version }} / ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
-        python-version: ['3.7']
-    steps:
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: '0'
-      - uses: goanpeca/setup-miniconda@v1
-        with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          activate-environment: matchms-dev
-          environment-file: conda/environment-dev.yml
-          condarc-file: conda/condarc.yml
-          auto-activate-base: false
-      - name: Conda info
-        shell: bash -l {0}
-        run: conda info
-      - name: Python info
-        shell: bash -l {0}
-        run: |
-          which python
-          python --version
-      - name: Conda list
-        shell: bash -l {0}
-        run: conda list
-      - name: Check style against standards using prospector
-        shell: bash -l {0}
-        run: prospector -o grouped -o pylint:pylint-report.txt
-      - name: Check whether import statements are used consistently
-        shell: bash -l {0}
-        run: isort --check-only --diff --conda-env matchms-dev --recursive --wrap-length 79 --lines-after-imports 2 --force-single-line --no-lines-before FUTURE --no-lines-before STDLIB --no-lines-before THIRDPARTY --no-lines-before FIRSTPARTY --no-lines-before LOCALFOLDER matchms/ tests/ integration-tests/
-      - name: Build
-        shell: bash -l {0}
-        run: |
-          python setup.py build
-      - name: Build documentation
-        shell: bash -l {0}
-        run: |
-          make coverage html
-        working-directory: readthedocs/
-        env:
-          SPHINXOPTS: '-n'  # enable nit-picky mode
-      - name: Check documentation coverage threshold
-        if: matrix.os == 'ubuntu-latest'
-        shell: bash -l {0}
-        run: |
-          cat readthedocs/_build/coverage/python.txt
-          UNCOVERED_MEMBERS=$(grep '*' readthedocs/_build/coverage/python.txt | wc -l)
-          UNCOVERED_MEMBERS_ALLOWED=25
-          if (( $UNCOVERED_MEMBERS > $UNCOVERED_MEMBERS_ALLOWED )) ; then echo "There are currently ${UNCOVERED_MEMBERS} uncovered members in the documentation, which is more than the ${UNCOVERED_MEMBERS_ALLOWED} allowed."; exit 1;fi
-          echo "The code is sufficiently documented with ${UNCOVERED_MEMBERS} uncovered members out of ${UNCOVERED_MEMBERS_ALLOWED} allowed.";
-      - name: Test
-        if: matrix.os != 'ubuntu-latest'
-        shell: bash -l {0}
-        run: |
-          python setup.py test
-      - name: Test with coverage
-        if: matrix.os == 'ubuntu-latest'
-        shell: bash -l {0}
-        run: |
-          pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml
-      - name: Correct coverage paths
-        if: matrix.os == 'ubuntu-latest'
-        run: sed -i "s+$PWD/++g" coverage.xml
-      - name: SonarCloud Scan
-        if: matrix.os == 'ubuntu-latest'
-        uses: sonarsource/sonarcloud-github-action@master
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index 89b7747..998008d 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -14,7 +14,74 @@ jobs:
         python-version: ['3.7']
     steps:
       - uses: actions/checkout@v2
+        with:
+          fetch-depth: '0'
       - uses: goanpeca/setup-miniconda@v1
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          activate-environment: matchms-dev
+          environment-file: conda/environment-dev.yml
+          condarc-file: conda/condarc.yml
+          auto-activate-base: false
+      - name: Conda info
+        shell: bash -l {0}
+        run: conda info
+      - name: Python info
+        shell: bash -l {0}
+        run: |
+          which python
+          python --version
+      - name: Conda list
+        shell: bash -l {0}
+        run: conda list
+      - name: Check style against standards using prospector
+        shell: bash -l {0}
+        run: prospector -o grouped -o pylint:pylint-report.txt
+      - name: Check whether import statements are used consistently
+        shell: bash -l {0}
+        run: isort --check-only --diff --conda-env matchms-dev --recursive --wrap-length 79 --lines-after-imports 2 --force-single-line --no-lines-before FUTURE --no-lines-before STDLIB --no-lines-before THIRDPARTY --no-lines-before FIRSTPARTY --no-lines-before LOCALFOLDER matchms/ tests/ integration-tests/
+      - name: Build
+        shell: bash -l {0}
+        run: |
+          python setup.py build
+      - name: Build documentation
+        shell: bash -l {0}
+        run: |
+          make coverage html
+        working-directory: readthedocs/
+        env:
+          SPHINXOPTS: '-n'  # enable nit-picky mode
+      - name: Check documentation coverage threshold
+        if: matrix.os == 'ubuntu-latest'
+        shell: bash -l {0}
+        run: |
+          cat readthedocs/_build/coverage/python.txt
+          UNCOVERED_MEMBERS=$(grep '*' readthedocs/_build/coverage/python.txt | wc -l)
+          UNCOVERED_MEMBERS_ALLOWED=25
+          if (( $UNCOVERED_MEMBERS > $UNCOVERED_MEMBERS_ALLOWED )) ; then echo "There are currently ${UNCOVERED_MEMBERS} uncovered members in the documentation, which is more than the ${UNCOVERED_MEMBERS_ALLOWED} allowed."; exit 1;fi
+          echo "The code is sufficiently documented with ${UNCOVERED_MEMBERS} uncovered members out of ${UNCOVERED_MEMBERS_ALLOWED} allowed.";
+      - name: Test
+        if: matrix.os != 'ubuntu-latest'
+        shell: bash -l {0}
+        run: |
+          python setup.py test
+      - name: Test with coverage
+        if: matrix.os == 'ubuntu-latest'
+        shell: bash -l {0}
+        run: |
+          pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml
+      - name: Correct coverage paths
+        if: matrix.os == 'ubuntu-latest'
+        run: sed -i "s+$PWD/++g" coverage.xml
+      - name: SonarCloud Scan
+        if: matrix.os == 'ubuntu-latest'
+        uses: sonarsource/sonarcloud-github-action@master
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+      - name: Create matchms-build environment
+        uses: goanpeca/setup-miniconda@v1
         with:
           activate-environment: matchms-build
           auto-activate-base: false

From 57856f93a1af1c845c682ccd7161f9418a377fa6 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Tue, 19 May 2020 23:34:03 +0200
Subject: [PATCH 03/31] remove python build badge

---
 README.rst | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/README.rst b/README.rst
index 2c6c10d..e59ffef 100644
--- a/README.rst
+++ b/README.rst
@@ -28,7 +28,7 @@ Vector representation and similarity measure for mass spectrometry data.
    * - **Other best practices**
      -
    * - Continuous integration
-     - |Python Build| |Anaconda Build| |Anaconda Publish|
+     - |Anaconda Build| |Anaconda Publish|
    * - Documentation
      - |ReadTheDocs Badge|
    * - Code Quality
@@ -75,10 +75,6 @@ Vector representation and similarity measure for mass spectrometry data.
    :target: https://sonarcloud.io/component_measures?id=matchms_matchms&metric=Coverage&view=list
    :alt: Sonarcloud Coverage
 
-.. |Python Build| image:: https://github.com/matchms/matchms/workflows/Python%20Build/badge.svg
-   :target: https://github.com/matchms/matchms/actions?query=workflow%3A%22Python%20Build%22
-   :alt: Python Build
-
 .. |Anaconda Build| image:: https://github.com/matchms/matchms/workflows/Anaconda%20Build/badge.svg
    :target: https://github.com/matchms/matchms/actions?query=workflow%3A%22Anaconda%20Build%22
    :alt: Anaconda Build

From aa4b27ccb1f903f864b462e26764271747be06cc Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Tue, 19 May 2020 23:38:29 +0200
Subject: [PATCH 04/31] bump to 0.3.2

---
 conda/meta.yaml        | 2 +-
 matchms/__version__.py | 2 +-
 setup.cfg              | 6 ++----
 3 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/conda/meta.yaml b/conda/meta.yaml
index 652c5a1..24075b9 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "matchms" %}
-{% set version = "0.3.1" %}
+{% set version = "0.3.2" %}
 
 package:
   name: {{ name|lower }}
diff --git a/matchms/__version__.py b/matchms/__version__.py
index e1424ed..73e3bb4 100644
--- a/matchms/__version__.py
+++ b/matchms/__version__.py
@@ -1 +1 @@
-__version__ = '0.3.1'
+__version__ = '0.3.2'
diff --git a/setup.cfg b/setup.cfg
index a276340..0ee7145 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.1
+current_version = 0.3.2
 
 [bumpversion:file:conda/meta.yaml]
 search = set version = "{current_version}"
@@ -13,8 +13,7 @@ replace = __version__ = '{new_version}'
 description-file = README.rst
 
 [aliases]
-# Define `python setup.py test`
-test=pytest
+test = pytest
 
 [coverage:run]
 branch = True
@@ -25,7 +24,6 @@ testpaths = tests integration-tests
 python_classes = *TestSuite
 junit_family = xunit2
 
-# Define `python setup.py build_sphinx`
 [build_sphinx]
 source-dir = docs
 build-dir = docs/_build

From f3aff59f133449fd5b64b0d7d3b84cf547cdb490 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Tue, 19 May 2020 23:44:37 +0200
Subject: [PATCH 05/31] update the changelog

---
 CHANGELOG.md | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d2f7fc9..4055f65 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,11 +7,24 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.3.2] - 2020-05-20
+
+### Changed
+
+- improve conda workflow [#244](https://github.com/matchms/matchms/pull/244)
+  - merge anaconda and python build workflows
+  - fix conda package install command in build workflow
+  - publish only on ubuntu machine
+
+### Removed
+
+- remove python build badge [#244](https://github.com/matchms/matchms/pull/244)
+
 ## [0.3.1] - 2020-05-19
 
 ### Added
 
-- improve conda package https://github.com/matchms/matchms/pull/225
+- improve conda package [#225](https://github.com/matchms/matchms/pull/225)
   - Build scripts for Windows and Unix(MacOS and Linux) systems
   - verify conda package after uploading to anaconda repository by installing it
   - conda package also includes `matchms/data` folder
@@ -29,9 +42,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - skip builds for Python 2.X
   - more flexible package versions
   - add deployment requirements to meta.yml
-- verify conda package https://github.com/matchms/matchms/pull/225
+- verify conda package [#225](https://github.com/matchms/matchms/pull/225)
   - use conda/environment.yml when building the package
-- split anaconda workflow https://github.com/matchms/matchms/pull/225
+- split anaconda workflow [#225](https://github.com/matchms/matchms/pull/225)
   - conda build: tests conda packages on every push and pull request
   - conda publish: publish and test conda package on release
   - update the developer instructions

From eda8b12c1ad380344c2b4755a9051fe3b096cbe0 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 09:34:26 +0200
Subject: [PATCH 06/31] handle data in setup.py

---
 conda/build.sh | 6 +++---
 setup.py       | 3 ++-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/conda/build.sh b/conda/build.sh
index 46144b1..49d65b2 100644
--- a/conda/build.sh
+++ b/conda/build.sh
@@ -5,6 +5,6 @@ env
 
 $PYTHON -m pip install --no-deps --ignore-installed . -vv
 
-# Copy data folder
-mkdir -p $PREFIX/site-packages/matchms/data
-cp matchms/data/* $PREFIX/site-packages/matchms/data/
+# # Copy data folder
+# mkdir -p $PREFIX/site-packages/matchms/data
+# cp matchms/data/* $PREFIX/site-packages/matchms/data/
diff --git a/setup.py b/setup.py
index 1e16383..d3b92a0 100644
--- a/setup.py
+++ b/setup.py
@@ -55,5 +55,6 @@
     ],
     extras_require={
         # see conda/environment.yml
-    }
+    },
+    package_data={'data': ['matchms/data/*.yaml']},
 )

From a6a39a34f2ff081155270c193267903be2138ddb Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 09:35:41 +0200
Subject: [PATCH 07/31] change conda info step while testing conda package
 build

---
 .github/workflows/conda_build.yml | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index 998008d..850ddc5 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -89,18 +89,17 @@ jobs:
           environment-file: conda/environment-build.yml
           miniconda-version: 'latest'
           python-version: ${{ matrix.python-version }}
-      - name: Show conda config
+      - name: Conda info
         shell: bash -l {0}
-        run: |
-          conda info
-          conda list
-          conda config --show-sources
-          conda config --show
+        run: conda info
       - name: Python info
         shell: bash -l {0}
         run: |
           which python
           python --version
+      - name: Conda list
+        shell: bash -l {0}
+        run: conda list
       - name: Build the conda package
         shell: bash -l {0}
         run: |

From 7fe99d2d7b35844582bc30ee2bfa2c409aa0fc64 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 09:54:06 +0200
Subject: [PATCH 08/31] automatically activate conda environments

---
 .github/workflows/conda_build.yml | 8 ++++----
 README.rst                        | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index 850ddc5..4042403 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -18,12 +18,12 @@ jobs:
           fetch-depth: '0'
       - uses: goanpeca/setup-miniconda@v1
         with:
-          auto-update-conda: true
+          auto-update-conda: false
           python-version: ${{ matrix.python-version }}
           activate-environment: matchms-dev
           environment-file: conda/environment-dev.yml
           condarc-file: conda/condarc.yml
-          auto-activate-base: false
+          auto-activate-base: true
       - name: Conda info
         shell: bash -l {0}
         run: conda info
@@ -84,8 +84,8 @@ jobs:
         uses: goanpeca/setup-miniconda@v1
         with:
           activate-environment: matchms-build
-          auto-activate-base: false
-          auto-update-conda: true
+          auto-activate-base: true
+          auto-update-conda: false
           environment-file: conda/environment-build.yml
           miniconda-version: 'latest'
           python-version: ${{ matrix.python-version }}
diff --git a/README.rst b/README.rst
index e59ffef..eb46ebe 100644
--- a/README.rst
+++ b/README.rst
@@ -187,7 +187,7 @@ installation of this conda package works with:
   conda install \
     --channel bioconda \
     --channel conda-forge \
-    --channel file://${CONDA_PREFIX}/output/noarch/ \
+    --channel file://${CONDA_PREFIX}/noarch/ \
     matchms
 
 To publish the package on anaconda cloud, do:

From 13d22934d978b7ed9327fe3eff144e7d0933175c Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 09:54:47 +0200
Subject: [PATCH 09/31] test generated conda package by installing it

---
 .github/workflows/conda_build.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index 4042403..d53297c 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -110,3 +110,11 @@ jobs:
             --channel bioconda --channel conda-forge \
             --croot $BUILD_FOLDER \
             ./conda
+      - name: Test local conda package
+        shell: bash -l {0}
+        run: |
+          conda install \
+            --channel bioconda \
+            --channel conda-forge \
+            --channel file://${BUILD_FOLDER}/noarch/ \
+            matchms

From 8859b04f0961969509dfa8b0229fba4d8032a8d3 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 09:56:33 +0200
Subject: [PATCH 10/31] remove conda/conda_build_config.yaml

---
 conda/conda_build_config.yaml | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 conda/conda_build_config.yaml

diff --git a/conda/conda_build_config.yaml b/conda/conda_build_config.yaml
deleted file mode 100644
index e69de29..0000000

From a4635fa7c787bae560f78b78ee434e12895980b3 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 10:16:52 +0200
Subject: [PATCH 11/31] add BUILD_FOLDER variable

---
 .github/workflows/conda_build.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index d53297c..3a92974 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -113,6 +113,7 @@ jobs:
       - name: Test local conda package
         shell: bash -l {0}
         run: |
+          export BUILD_FOLDER=/tmp/matchms/_build
           conda install \
             --channel bioconda \
             --channel conda-forge \

From a9d02d5cf800b20220c0c2ff11baa5f11a0fae78 Mon Sep 17 00:00:00 2001
From: Faruk D <fdiblen@users.noreply.github.com>
Date: Wed, 20 May 2020 10:17:21 +0200
Subject: [PATCH 12/31] Update setup.py

Co-authored-by: Stefan Verhoeven <s.verhoeven@esciencecenter.nl>
---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index d3b92a0..c9f16cf 100644
--- a/setup.py
+++ b/setup.py
@@ -56,5 +56,5 @@
     extras_require={
         # see conda/environment.yml
     },
-    package_data={'data': ['matchms/data/*.yaml']},
+    package_data={'matchms': ['data/*.yaml']},
 )

From 59001cfea6627274c98fef3ddefed4ca737d9fb2 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 10:45:18 +0200
Subject: [PATCH 13/31] list conda environments for debugging

---
 .github/workflows/conda_build.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index 3a92974..7b2a079 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -91,7 +91,8 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Conda info
         shell: bash -l {0}
-        run: conda info
+        run: |
+          conda env list
       - name: Python info
         shell: bash -l {0}
         run: |

From 57f7704d2e78d006660723cf0c539e8bf776ac00 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 10:47:47 +0200
Subject: [PATCH 14/31] remove the build step

---
 .github/workflows/conda_build.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index 7b2a079..6937479 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -41,10 +41,6 @@ jobs:
       - name: Check whether import statements are used consistently
         shell: bash -l {0}
         run: isort --check-only --diff --conda-env matchms-dev --recursive --wrap-length 79 --lines-after-imports 2 --force-single-line --no-lines-before FUTURE --no-lines-before STDLIB --no-lines-before THIRDPARTY --no-lines-before FIRSTPARTY --no-lines-before LOCALFOLDER matchms/ tests/ integration-tests/
-      - name: Build
-        shell: bash -l {0}
-        run: |
-          python setup.py build
       - name: Build documentation
         shell: bash -l {0}
         run: |

From eb30213d531022f735a7db013361409bc8609a96 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 10:49:04 +0200
Subject: [PATCH 15/31] deactivate previous environment before creating a new
 environment

---
 .github/workflows/conda_build.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index 6937479..b6c342f 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -76,6 +76,10 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+      - name: Deactivate matchms-dev environment
+        shell: bash -l {0}
+        run: |
+          conda deactivate
       - name: Create matchms-build environment
         uses: goanpeca/setup-miniconda@v1
         with:

From d2fc329a9e693027609a055b8db9504aa4c53e38 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 11:17:54 +0200
Subject: [PATCH 16/31] data is added by setup.py, build scripts ware removed

---
 conda/bld.bat   |  6 ------
 conda/build.sh  | 10 ----------
 conda/meta.yaml |  1 +
 setup.py        |  2 +-
 4 files changed, 2 insertions(+), 17 deletions(-)
 delete mode 100644 conda/bld.bat
 delete mode 100644 conda/build.sh

diff --git a/conda/bld.bat b/conda/bld.bat
deleted file mode 100644
index b7c1428..0000000
--- a/conda/bld.bat
+++ /dev/null
@@ -1,6 +0,0 @@
-"%PYTHON%" -m pip install --no-deps --ignore-installed . -vv
-
-mkdir %PREFIX%\site-packages\matchms\data
-copy matchms\data\* %PREFIX%\site-packages\matchms\data\
-
-if errorlevel 1 exit 1
diff --git a/conda/build.sh b/conda/build.sh
deleted file mode 100644
index 49d65b2..0000000
--- a/conda/build.sh
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/bin/bash
-
-# Show environment variables
-env
-
-$PYTHON -m pip install --no-deps --ignore-installed . -vv
-
-# # Copy data folder
-# mkdir -p $PREFIX/site-packages/matchms/data
-# cp matchms/data/* $PREFIX/site-packages/matchms/data/
diff --git a/conda/meta.yaml b/conda/meta.yaml
index 24075b9..ad477ad 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -18,6 +18,7 @@ build:
   preserve_egg_dir: True
   number: 0
   skip: True # [py2k]
+  script: {{PYTHON}} -m pip install --no-deps --ignore-installed . -vv
 
 requirements:
   build:
diff --git a/setup.py b/setup.py
index c9f16cf..4114d16 100644
--- a/setup.py
+++ b/setup.py
@@ -56,5 +56,5 @@
     extras_require={
         # see conda/environment.yml
     },
-    package_data={'matchms': ['data/*.yaml']},
+    package_data={"matchms": ["data/*.yaml"]},
 )

From 9abd42aa318a423cd81a87c8da19a8390f8d334c Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 11:25:49 +0200
Subject: [PATCH 17/31] remove condarc

---
 .github/workflows/conda_build.yml | 7 +++----
 conda/condarc.yml                 | 0
 conda/meta.yaml                   | 2 +-
 3 files changed, 4 insertions(+), 5 deletions(-)
 delete mode 100644 conda/condarc.yml

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index b6c342f..4227bc9 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -18,12 +18,11 @@ jobs:
           fetch-depth: '0'
       - uses: goanpeca/setup-miniconda@v1
         with:
-          auto-update-conda: false
-          python-version: ${{ matrix.python-version }}
           activate-environment: matchms-dev
-          environment-file: conda/environment-dev.yml
-          condarc-file: conda/condarc.yml
           auto-activate-base: true
+          auto-update-conda: false
+          environment-file: conda/environment-dev.yml
+          python-version: ${{ matrix.python-version }}
       - name: Conda info
         shell: bash -l {0}
         run: conda info
diff --git a/conda/condarc.yml b/conda/condarc.yml
deleted file mode 100644
index e69de29..0000000
diff --git a/conda/meta.yaml b/conda/meta.yaml
index ad477ad..0a4faac 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -18,7 +18,7 @@ build:
   preserve_egg_dir: True
   number: 0
   skip: True # [py2k]
-  script: {{PYTHON}} -m pip install --no-deps --ignore-installed . -vv
+  script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . -vv
 
 requirements:
   build:

From 27467bde38c196306e117f00b2f4ad67ccd94960 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 11:33:35 +0200
Subject: [PATCH 18/31] use defaults for conda ction

---
 .github/workflows/conda_build.yml   | 5 -----
 .github/workflows/conda_publish.yml | 6 ------
 2 files changed, 11 deletions(-)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index 4227bc9..4a681ee 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -19,8 +19,6 @@ jobs:
       - uses: goanpeca/setup-miniconda@v1
         with:
           activate-environment: matchms-dev
-          auto-activate-base: true
-          auto-update-conda: false
           environment-file: conda/environment-dev.yml
           python-version: ${{ matrix.python-version }}
       - name: Conda info
@@ -83,10 +81,7 @@ jobs:
         uses: goanpeca/setup-miniconda@v1
         with:
           activate-environment: matchms-build
-          auto-activate-base: true
-          auto-update-conda: false
           environment-file: conda/environment-build.yml
-          miniconda-version: 'latest'
           python-version: ${{ matrix.python-version }}
       - name: Conda info
         shell: bash -l {0}
diff --git a/.github/workflows/conda_publish.yml b/.github/workflows/conda_publish.yml
index 1f7cb64..4c6333e 100644
--- a/.github/workflows/conda_publish.yml
+++ b/.github/workflows/conda_publish.yml
@@ -19,10 +19,7 @@ jobs:
       - uses: goanpeca/setup-miniconda@v1
         with:
           activate-environment: matchms-build
-          auto-activate-base: false
-          auto-update-conda: true
           environment-file: conda/environment-build.yml
-          miniconda-version: 'latest'
           python-version: ${{ matrix.python-version }}
       - name: Show conda config
         shell: bash -l {0}
@@ -54,10 +51,7 @@ jobs:
       - uses: goanpeca/setup-miniconda@v1
         with:
           activate-environment: matchms-test
-          auto-activate-base: false
-          auto-update-conda: true
           channels: conda-forge,bioconda,nlesc
-          miniconda-version: 'latest'
           python-version: ${{ matrix.python-version }}
       - name: Show conda config
         shell: bash -l {0}

From aa2f9a0929ea5a707c5a7dc25a4c65167512feb5 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 11:44:48 +0200
Subject: [PATCH 19/31] add Python to action names

---
 .github/workflows/conda_build.yml   | 2 +-
 .github/workflows/conda_publish.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index 4a681ee..81ef428 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -5,7 +5,7 @@ on: [push, pull_request]
 jobs:
 
   build:
-    name: ${{ matrix.python-version }} / ${{ matrix.os }}
+    name: Python ${{ matrix.python-version }} / ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
diff --git a/.github/workflows/conda_publish.yml b/.github/workflows/conda_publish.yml
index 4c6333e..55faeb7 100644
--- a/.github/workflows/conda_publish.yml
+++ b/.github/workflows/conda_publish.yml
@@ -7,7 +7,7 @@ on:
 jobs:
 
   publish:
-    name: ${{ matrix.python-version }} / ${{ matrix.os }}
+    name: Python ${{ matrix.python-version }} / ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false

From bb75b601c41944dcd96d412887625120a40f2a62 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 12:25:17 +0200
Subject: [PATCH 20/31] split workflows and test the conda package on
 windows/unix separately

---
 .github/workflows/conda_build.yml   | 22 +++++++++++++++++++++-
 .github/workflows/conda_publish.yml |  9 +++++++++
 2 files changed, 30 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index 81ef428..75535d0 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -4,7 +4,7 @@ on: [push, pull_request]
 
 jobs:
 
-  build:
+  analysis:
     name: Python ${{ matrix.python-version }} / ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
@@ -73,6 +73,15 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+
+  build:
+    name: Python ${{ matrix.python-version }} / ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    needs: analysis
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: '0'
       - name: Deactivate matchms-dev environment
         shell: bash -l {0}
         run: |
@@ -106,6 +115,7 @@ jobs:
             --croot $BUILD_FOLDER \
             ./conda
       - name: Test local conda package
+        if: matrix.os != 'windows-latest'
         shell: bash -l {0}
         run: |
           export BUILD_FOLDER=/tmp/matchms/_build
@@ -114,3 +124,13 @@ jobs:
             --channel conda-forge \
             --channel file://${BUILD_FOLDER}/noarch/ \
             matchms
+      - name: Test local conda package
+        if: matrix.os == 'windows-latest'
+        shell: bash -l {0}
+        run: |
+          export BUILD_FOLDER=%TMPDIR%\matchms\_build
+          conda install \
+            --channel bioconda \
+            --channel conda-forge \
+            --channel file:\\${BUILD_FOLDER}\noarch\ \
+            matchms
diff --git a/.github/workflows/conda_publish.yml b/.github/workflows/conda_publish.yml
index 55faeb7..70fd643 100644
--- a/.github/workflows/conda_publish.yml
+++ b/.github/workflows/conda_publish.yml
@@ -48,6 +48,15 @@ jobs:
         run: |
           export BUILD_FOLDER=/tmp/matchms/_build
           anaconda --token ${{ secrets.ANACONDA_TOKEN }} upload --user nlesc --force $BUILD_FOLDER/noarch/*.tar.bz2
+
+  testpublished:
+    name: Python ${{ matrix.python-version }} / ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    needs: publish
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: '0'
       - uses: goanpeca/setup-miniconda@v1
         with:
           activate-environment: matchms-test

From d1cc37d96574f36fd221a5973699f09368c9db54 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 12:28:20 +0200
Subject: [PATCH 21/31] update temp folder for windows

---
 .github/workflows/conda_build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index 75535d0..b90cbf9 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -128,7 +128,7 @@ jobs:
         if: matrix.os == 'windows-latest'
         shell: bash -l {0}
         run: |
-          export BUILD_FOLDER=%TMPDIR%\matchms\_build
+          export BUILD_FOLDER=%TEMP%\matchms\_build
           conda install \
             --channel bioconda \
             --channel conda-forge \

From 7f9112c47e0da8dd9141171a4f60b224bfd1c78e Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 12:36:34 +0200
Subject: [PATCH 22/31] update CHANGELOG.md

---
 CHANGELOG.md | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8d6855d..5784adc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,8 +7,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Unreleased
 
-- [diff](https://github.com/matchms/matchms/compare/0.3.1...HEAD) since 0.3.1 
-
 ### Added
 
 - ...
@@ -23,20 +21,32 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Removed
 
-- Moved ``spec2vec`` similarity related functionality from ``matchms`` to https://github.com/iomega/spec2vec   
 
 ## [0.3.2] - 2020-05-20
 
+- [All changes](https://github.com/matchms/matchms/compare/0.3.1...HEAD) since 0.3.1
+
 ### Changed
 
 - improve conda workflow [#244](https://github.com/matchms/matchms/pull/244)
   - merge anaconda and python build workflows
   - fix conda package install command in build workflow
   - publish only on ubuntu machine
+- data folder is handled by setup.py but not meta.yml
+- split workflows into two parts
+- install conda package generated by the workflow
+- test conda packages on windows and unix separately
+- update workflow names
+- use default settings for conda action
 
 ### Removed
 
 - remove python build badge [#244](https://github.com/matchms/matchms/pull/244)
+- Moved ``spec2vec`` similarity related functionality from ``matchms`` to [iomega/spec2vec](https://github.com/iomega/spec2vec)
+- removed build step in build workflow
+- removed conda build scripts: conda/build.sh and conda/bld.bat
+- removed conda/condarc.yml
+- removed conda_build_config.yaml
 
 ## [0.3.1] - 2020-05-19
 

From 49e2b5b7e5c4f0d223c5eb1cb7f0b01a830f4929 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 15:00:43 +0200
Subject: [PATCH 23/31] add strategy section to build workflow

---
 .github/workflows/conda_build.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index b90cbf9..673bfc8 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -78,6 +78,11 @@ jobs:
     name: Python ${{ matrix.python-version }} / ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     needs: analysis
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
+        python-version: ['3.7']
     steps:
       - uses: actions/checkout@v2
         with:

From 81ef3cc722dfc1e597f89b5fe84ae7858f923e64 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 15:01:45 +0200
Subject: [PATCH 24/31] add strategy section to publish workflow

---
 .github/workflows/conda_publish.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/conda_publish.yml b/.github/workflows/conda_publish.yml
index 70fd643..3a82738 100644
--- a/.github/workflows/conda_publish.yml
+++ b/.github/workflows/conda_publish.yml
@@ -53,6 +53,11 @@ jobs:
     name: Python ${{ matrix.python-version }} / ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     needs: publish
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ['ubuntu-latest']
+        python-version: ['3.7']
     steps:
       - uses: actions/checkout@v2
         with:

From 2062f7af9f25772b4ddb7a7d8f2eadffbea14e90 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 15:19:02 +0200
Subject: [PATCH 25/31] make distinction for workflow jobs using different
 names

---
 .github/workflows/conda_build.yml   | 4 ++--
 .github/workflows/conda_publish.yml | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index 673bfc8..4ad77f4 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -5,7 +5,7 @@ on: [push, pull_request]
 jobs:
 
   analysis:
-    name: Python ${{ matrix.python-version }} / ${{ matrix.os }}
+    name: Analysis-Python ${{ matrix.python-version }} / ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -75,7 +75,7 @@ jobs:
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
   build:
-    name: Python ${{ matrix.python-version }} / ${{ matrix.os }}
+    name: Build - Python ${{ matrix.python-version }} / ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     needs: analysis
     strategy:
diff --git a/.github/workflows/conda_publish.yml b/.github/workflows/conda_publish.yml
index 3a82738..e4d16d4 100644
--- a/.github/workflows/conda_publish.yml
+++ b/.github/workflows/conda_publish.yml
@@ -7,7 +7,7 @@ on:
 jobs:
 
   publish:
-    name: Python ${{ matrix.python-version }} / ${{ matrix.os }}
+    name: Publish-Python ${{ matrix.python-version }} / ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -50,7 +50,7 @@ jobs:
           anaconda --token ${{ secrets.ANACONDA_TOKEN }} upload --user nlesc --force $BUILD_FOLDER/noarch/*.tar.bz2
 
   testpublished:
-    name: Python ${{ matrix.python-version }} / ${{ matrix.os }}
+    name: Test Published-Python ${{ matrix.python-version }} / ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     needs: publish
     strategy:

From 2399b7f89728fc500ed876003dc308018caf8322 Mon Sep 17 00:00:00 2001
From: "Jurriaan H. Spaaks" <j.spaaks@esciencecenter.nl>
Date: Wed, 20 May 2020 16:03:34 +0200
Subject: [PATCH 26/31] updated conda build files

---
 .github/workflows/conda_build.yml   |  6 +++++-
 .github/workflows/conda_publish.yml |  6 ++----
 README.rst                          | 12 +++++++-----
 conda/anaconda-client-env           |  0
 4 files changed, 14 insertions(+), 10 deletions(-)
 delete mode 100644 conda/anaconda-client-env

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index 4ad77f4..53ee30d 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -97,9 +97,13 @@ jobs:
           activate-environment: matchms-build
           environment-file: conda/environment-build.yml
           python-version: ${{ matrix.python-version }}
-      - name: Conda info
+      - name: Show conda config
         shell: bash -l {0}
         run: |
+          conda info
+          conda list
+          conda config --show-sources
+          conda config --show
           conda env list
       - name: Python info
         shell: bash -l {0}
diff --git a/.github/workflows/conda_publish.yml b/.github/workflows/conda_publish.yml
index e4d16d4..497dbad 100644
--- a/.github/workflows/conda_publish.yml
+++ b/.github/workflows/conda_publish.yml
@@ -64,7 +64,8 @@ jobs:
           fetch-depth: '0'
       - uses: goanpeca/setup-miniconda@v1
         with:
-          activate-environment: matchms-test
+          activate-environment: matchms-dev
+          environment-file: conda/environment-dev.yml
           channels: conda-forge,bioconda,nlesc
           python-version: ${{ matrix.python-version }}
       - name: Show conda config
@@ -78,9 +79,6 @@ jobs:
         shell: bash -l {0}
         run: |
           conda install -c bioconda -c conda-forge -c nlesc matchms
-      - name: Install development dependencies
-        shell: bash -l {0}
-        run: python -m pip install -r conda/requirements-dev.txt
       - name: Test the installed conda package
         shell: bash -l {0}
         run: |
diff --git a/README.rst b/README.rst
index eb46ebe..8bfc72b 100644
--- a/README.rst
+++ b/README.rst
@@ -58,10 +58,6 @@ Vector representation and similarity measure for mass spectrometry data.
    :target: https://bestpractices.coreinfrastructure.org/projects/3792
    :alt: CII Best Practices Badge
 
-.. |GitHub Actions Badge| image:: https://github.com/matchms/matchms/workflows/Build%20matchms/badge.svg
-   :target: https://github.com/matchms/matchms/actions?query=workflow%3A%22Build+matchms%22
-   :alt: GitHub Actions Badge
-
 .. |ReadTheDocs Badge| image:: https://readthedocs.org/projects/matchms/badge/?version=latest
     :alt: Documentation Status
     :scale: 100%
@@ -184,6 +180,12 @@ installation of this conda package works with:
 
 .. code-block:: console
 
+  # make a clean environment
+  conda deactivate
+  cd $(mktemp -d)
+  conda env create --name test python=3.7
+  conda activate test
+
   conda install \
     --channel bioconda \
     --channel conda-forge \
@@ -199,7 +201,7 @@ To publish the package on anaconda cloud, do:
 where ``secrets.ANACONDA_TOKEN`` is a token to be generated on the Anaconda Cloud website. This secret should be added to GitHub repository.
 
 
-To remove matchms package:
+To remove matchms package from the active environment:
 
 .. code-block:: console
 
diff --git a/conda/anaconda-client-env b/conda/anaconda-client-env
deleted file mode 100644
index e69de29..0000000

From c023bd2b23d430c873a28b59df473188399a42d1 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 16:12:20 +0200
Subject: [PATCH 27/31] change strategy - needs order in build

---
 .github/workflows/conda_build.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index 4ad77f4..6b2f3d2 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -75,14 +75,13 @@ jobs:
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
   build:
-    name: Build - Python ${{ matrix.python-version }} / ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
-    needs: analysis
     strategy:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
         python-version: ['3.7']
+    runs-on: ${{ matrix.os }}
+    needs: analysis
     steps:
       - uses: actions/checkout@v2
         with:

From 61fdfabda3c212725c07b456ad89b783c34ad276 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 16:20:31 +0200
Subject: [PATCH 28/31] test build only on ubuntu

---
 .github/workflows/conda_build.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index f0581af..2b480cb 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -78,7 +78,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
+        os: ['ubuntu-latest']
         python-version: ['3.7']
     runs-on: ${{ matrix.os }}
     needs: analysis
@@ -122,7 +122,7 @@ jobs:
             --channel bioconda --channel conda-forge \
             --croot $BUILD_FOLDER \
             ./conda
-      - name: Test local conda package
+      - name: Test local conda package on unix
         if: matrix.os != 'windows-latest'
         shell: bash -l {0}
         run: |
@@ -132,7 +132,7 @@ jobs:
             --channel conda-forge \
             --channel file://${BUILD_FOLDER}/noarch/ \
             matchms
-      - name: Test local conda package
+      - name: Test local conda package on windows
         if: matrix.os == 'windows-latest'
         shell: bash -l {0}
         run: |

From 3cde0e70586d6dfb063bea0697400d182713836a Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 16:21:57 +0200
Subject: [PATCH 29/31] remove deactivate step

---
 .github/workflows/conda_build.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index 2b480cb..6a0dbbc 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -86,10 +86,6 @@ jobs:
       - uses: actions/checkout@v2
         with:
           fetch-depth: '0'
-      - name: Deactivate matchms-dev environment
-        shell: bash -l {0}
-        run: |
-          conda deactivate
       - name: Create matchms-build environment
         uses: goanpeca/setup-miniconda@v1
         with:

From 41f2852c046fb516b014aa0812184e8c981e5ae7 Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 16:28:12 +0200
Subject: [PATCH 30/31] test the build workflow as a single job

---
 .github/workflows/conda_build.yml | 52 +++++++++++++++++++++++++------
 1 file changed, 43 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index 6a0dbbc..aed105a 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -74,15 +74,15 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
-  build:
-    strategy:
-      fail-fast: false
-      matrix:
-        os: ['ubuntu-latest']
-        python-version: ['3.7']
-    runs-on: ${{ matrix.os }}
-    needs: analysis
-    steps:
+  # build:
+  #   strategy:
+  #     fail-fast: false
+  #     matrix:
+  #       os: ['ubuntu-latest']
+  #       python-version: ['3.7']
+  #   runs-on: ${{ matrix.os }}
+  #   needs: analysis
+  #   steps:
       - uses: actions/checkout@v2
         with:
           fetch-depth: '0'
@@ -118,6 +118,40 @@ jobs:
             --channel bioconda --channel conda-forge \
             --croot $BUILD_FOLDER \
             ./conda
+
+  # testpackage:
+  #   strategy:
+  #     fail-fast: false
+  #     matrix:
+  #       os: ['ubuntu-latest']
+  #       python-version: ['3.7']
+  #   runs-on: ${{ matrix.os }}
+  #   needs: build
+  #   steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: '0'
+      - name: Create a test environment to test the package
+        uses: goanpeca/setup-miniconda@v1
+        with:
+          activate-environment: matchms-test
+          python-version: ${{ matrix.python-version }}
+      - name: Show conda config
+        shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+          conda config --show-sources
+          conda config --show
+          conda env list
+      - name: Python info
+        shell: bash -l {0}
+        run: |
+          which python
+          python --version
+      - name: Conda list
+        shell: bash -l {0}
+        run: conda list
       - name: Test local conda package on unix
         if: matrix.os != 'windows-latest'
         shell: bash -l {0}

From b18026d583338329df2f67e59a1e8ae07436d89d Mon Sep 17 00:00:00 2001
From: Faruk D <f.diblen@esciencecenter.nl>
Date: Wed, 20 May 2020 16:39:14 +0200
Subject: [PATCH 31/31] remove extra checkouts

---
 .github/workflows/conda_build.yml | 24 ------------------------
 1 file changed, 24 deletions(-)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index aed105a..8f6cd7b 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -74,18 +74,6 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
-  # build:
-  #   strategy:
-  #     fail-fast: false
-  #     matrix:
-  #       os: ['ubuntu-latest']
-  #       python-version: ['3.7']
-  #   runs-on: ${{ matrix.os }}
-  #   needs: analysis
-  #   steps:
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: '0'
       - name: Create matchms-build environment
         uses: goanpeca/setup-miniconda@v1
         with:
@@ -119,18 +107,6 @@ jobs:
             --croot $BUILD_FOLDER \
             ./conda
 
-  # testpackage:
-  #   strategy:
-  #     fail-fast: false
-  #     matrix:
-  #       os: ['ubuntu-latest']
-  #       python-version: ['3.7']
-  #   runs-on: ${{ matrix.os }}
-  #   needs: build
-  #   steps:
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: '0'
       - name: Create a test environment to test the package
         uses: goanpeca/setup-miniconda@v1
         with: