From bd38bbfaa3f16d847694faca1bbd0f0871660f6c Mon Sep 17 00:00:00 2001 From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com> Date: Mon, 9 Dec 2024 10:33:53 +0100 Subject: [PATCH 1/6] typo fix in example --- src/pynxtools/nomad/examples/iv_temp/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pynxtools/nomad/examples/iv_temp/README.md b/src/pynxtools/nomad/examples/iv_temp/README.md index 53dd7e055..b089e32f3 100644 --- a/src/pynxtools/nomad/examples/iv_temp/README.md +++ b/src/pynxtools/nomad/examples/iv_temp/README.md @@ -4,7 +4,7 @@ This is an example of a PID controlled sensor sweep scan. The temperature is set using a PID controller. Then, for the set temperature, a voltage sweep is performed. For each of the voltages, the current is measured. This is repeated for a given list of temperatures. -This specific data was captured using a Bluesky controlled system. This was then saved into a binary file using Pickle. This example illustrates how such a dataset could be converted using the [`JSONMapReader`](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/src/pynxtools/dataconverter/readers/json_map) of the NOMAD plugin [`pynxtools`](https://github.com/FAIRmat-NFDI/pynxtools-xps). +This specific data was captured using a Bluesky controlled system. This was then saved into a binary file using Pickle. This example illustrates how such a dataset could be converted using the [`JSONMapReader`](https://github.com/FAIRmat-NFDI/pynxtools/tree/master/src/pynxtools/dataconverter/readers/json_map) of the NOMAD plugin [`pynxtools`](https://github.com/FAIRmat-NFDI/pynxtools). The data is mapped on to a Nexus application definition for temperature-dependent IV curve measurements, [NXiv_temp](https://fairmat-nfdi.github.io/nexus_definitions/classes/contributed_definitions/NXiv_temp.html). # Viewing uploaded data From 1c9d1cb08fe4cafae1197770fcadb3917db340c8 Mon Sep 17 00:00:00 2001 From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com> Date: Mon, 9 Dec 2024 10:35:16 +0100 Subject: [PATCH 2/6] add reference and extra for pynxtools-igor --- docs/reference/plugins.md | 8 ++++++-- pyproject.toml | 5 ++++- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/docs/reference/plugins.md b/docs/reference/plugins.md index ab5b32391..ccd1bbe2b 100644 --- a/docs/reference/plugins.md +++ b/docs/reference/plugins.md @@ -1,5 +1,5 @@ # Plugins -There are a number of plugins available for pynxtools that are maintained within FAIRmat. These are extensions of pynxtools used for reading data of specific experimental techniques. +There are a number of plugins available for pynxtools that are maintained within FAIRmat. These are extensions of pynxtools used for reading data of specific experimental techniques and/or file formats. ### Photoemission spectroscopy - [**pynxtools-mpes**](https://github.com/FAIRmat-NFDI/pynxtools-mpes): A reader for multi-dimensional photoelectron spectroscopy (MPES) data. @@ -20,8 +20,12 @@ There are a number of plugins available for pynxtools that are maintained within - [**pynxtools-stm**](https://github.com/FAIRmat-NFDI/pynxtools-stm): A reader for scanning tunneling microscopy (SPM) and spectroscopy (STS) data. ### X-ray diffraction -- [**pynxtools-xrd**](https://github.com/FAIRmat-NFDI/pynxtools-raman): A reader for X-ray diffraction data. +- [**pynxtools-xrd**](https://github.com/FAIRmat-NFDI/pynxtools-xrd): A reader for X-ray diffraction data. + ### Others +- [**pynxtools-igor**](https://github.com/FAIRmat-NFDI/pynxtools-igor): A general reader for [Igor Pro](https://www.wavemetrics.com/) Binary Wave data. + + ## Installation diff --git a/pyproject.toml b/pyproject.toml index 6d74932e0..4ad2bdc24 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -64,7 +64,7 @@ dev = [ "pre-commit", ] convert = [ - "pynxtools[apm,em,mpes,xps,stm,xrd,ellips,raman]", + "pynxtools[apm,ellips,em,igor,mpes,stm,xps,xrd,raman]", ] apm = [ @@ -76,6 +76,9 @@ ellips = [ em = [ "pynxtools-em>=0.3.1", ] +igor = [ + "pynxtools-igor>=0.1.0", +] mpes = [ "pynxtools-mpes>=0.2.1", ] From 3742c0879e116313b1c2c1c27e61c61298b409da Mon Sep 17 00:00:00 2001 From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com> Date: Mon, 9 Dec 2024 10:37:11 +0100 Subject: [PATCH 3/6] link for pynxtools-igor docs --- docs/reference/plugins.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/reference/plugins.md b/docs/reference/plugins.md index ccd1bbe2b..94e8432ac 100644 --- a/docs/reference/plugins.md +++ b/docs/reference/plugins.md @@ -23,7 +23,7 @@ There are a number of plugins available for pynxtools that are maintained within - [**pynxtools-xrd**](https://github.com/FAIRmat-NFDI/pynxtools-xrd): A reader for X-ray diffraction data. ### Others -- [**pynxtools-igor**](https://github.com/FAIRmat-NFDI/pynxtools-igor): A general reader for [Igor Pro](https://www.wavemetrics.com/) Binary Wave data. +- [**pynxtools-igor**](https://github.com/FAIRmat-NFDI/pynxtools-igor): A general reader for [Igor Pro](https://www.wavemetrics.com/) Binary Wave data. Documentation can be found [here](https://fairmat-nfdi.github.io/pynxtools-igor/). From bbd882327f80b8fa405848cfee278fc0bc4b4a4e Mon Sep 17 00:00:00 2001 From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com> Date: Mon, 9 Dec 2024 10:38:03 +0100 Subject: [PATCH 4/6] order plugins in convert extra --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 4ad2bdc24..0efa43c49 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -64,7 +64,7 @@ dev = [ "pre-commit", ] convert = [ - "pynxtools[apm,ellips,em,igor,mpes,stm,xps,xrd,raman]", + "pynxtools[apm,ellips,em,igor,mpes,raman,stm,xps,xrd]", ] apm = [ From 9818fe2fb5c9a59288469ddf4b14d4bc7a0f9dc9 Mon Sep 17 00:00:00 2001 From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com> Date: Mon, 9 Dec 2024 10:40:29 +0100 Subject: [PATCH 5/6] add pynx-igor to plugin tests --- .github/workflows/plugin_test.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/plugin_test.yaml b/.github/workflows/plugin_test.yaml index b62aaf17d..cea3a5451 100644 --- a/.github/workflows/plugin_test.yaml +++ b/.github/workflows/plugin_test.yaml @@ -28,7 +28,9 @@ jobs: tests_to_run: tests/. - plugin: pynxtools-em branch: main - tests_to_run: tests/. + - plugin: pynxtools-igor + branch: main + tests_to_run: tests/. - plugin: pynxtools-mpes branch: main tests_to_run: tests/. From 8f019508c1bb39d50071c7ff86d5b53a6b06ba34 Mon Sep 17 00:00:00 2001 From: Lukas Pielsticker <50139597+lukaspie@users.noreply.github.com> Date: Mon, 9 Dec 2024 10:41:41 +0100 Subject: [PATCH 6/6] fix missing value for em plugin tests --- .github/workflows/plugin_test.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/plugin_test.yaml b/.github/workflows/plugin_test.yaml index cea3a5451..ab0798dda 100644 --- a/.github/workflows/plugin_test.yaml +++ b/.github/workflows/plugin_test.yaml @@ -28,6 +28,7 @@ jobs: tests_to_run: tests/. - plugin: pynxtools-em branch: main + tests_to_run: tests/. - plugin: pynxtools-igor branch: main tests_to_run: tests/.